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<h3 style="margin-top: 20px; margin-bottom: 10px;">

Étienne Mollier pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/spades" style="color: #1068bf; text-decoration: none;">Debian Med / spades</a>

</h3>

<h4 style="margin-top: 10px; margin-bottom: 10px;">

Commits:

</h4>

<ul>

<li>

<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653" style="color: #1068bf; text-decoration: none;">3d6cb8fc</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2022-07-24T07:28:33+02:00</i>

</div>

<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 3.15.5+dfsg</pre>

</li>

</ul>

<h4 style="margin-top: 10px; margin-bottom: 10px;">17 changed files:</h4>

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<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d" style="color: #1068bf; text-decoration: none;">

README.md

</a>

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<li class="file-stats">

<a href="#ae55101b54ce2616006582a65f21f81a27f56ef0" style="color: #1068bf; text-decoration: none;">

assembler/VERSION

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<li class="file-stats">

<a href="#a9849095d161d6172a4b8c397180ac07a1c37ec4" style="color: #1068bf; text-decoration: none;">

assembler/changelog.html

</a>

</li>

<li class="file-stats">

<a href="#fe7fdbbf8b2079ee15a0add300260abc27048a3e" style="color: #1068bf; text-decoration: none;">

assembler/manual.html

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<li class="file-stats">

<a href="#dcd694f38b9d988eef66a5f4f147c3bf07985834" style="color: #1068bf; text-decoration: none;">

assembler/src/cmake/pack.cmake

</a>

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<a href="#2461f718207d4b6e71915c3d925029ccda6cfcb3" style="color: #1068bf; text-decoration: none;">

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assembler/src/common/assembly_graph/handlers/used_edge_handler.hpp

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<a href="#6b87519efcf2bfa28c1e019b7d831798dcad0805" style="color: #1068bf; text-decoration: none;">

assembler/src/common/modules/alignment/pacbio/gap_filler.hpp

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<a href="#f62d3fc9e2b1b443c5e8c8b35bcdd58889b9f02b" style="color: #1068bf; text-decoration: none;">

assembler/src/projects/spades/contig_output_stage.cpp

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<a href="#a01bec1175b6b4bf495eef1a6cf54c7ee9a7b3f4" style="color: #1068bf; text-decoration: none;">

assembler/src/projects/spades/domain_matcher.cpp

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<a href="#cae247ed2a05b3b84c463e1573071c9fa168bdbe" style="color: #1068bf; text-decoration: none;">

assembler/src/spades_pipeline/options_parser.py

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<a href="#066017f8828ed241ff09ef4a975cb1f2d4f6be77" style="color: #1068bf; text-decoration: none;">

assembler/src/spades_pipeline/stages/correction_stage.py

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<a href="#4ca7358cd786dc7d88506f147334f9435130d750" style="color: #1068bf; text-decoration: none;">

assembler/src/spades_pipeline/stages/error_correction_stage.py

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<a href="#ed083a5a55c9cf1416864acf5c6f9b2612dde905" style="color: #1068bf; text-decoration: none;">

assembler/src/spades_pipeline/stages/pipeline.py

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−

assembler/src/spades_pipeline/stages/scaffold_correction_stage.py

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<a href="#e7d52fc6222d2879798307c613ccc5ac8e5e671a" style="color: #1068bf; text-decoration: none;">

assembler/src/spades_pipeline/stages/spades_iteration_stage.py

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<a href="#4ddada5bb56cf32c7e7459698418532494c64c21" style="color: #1068bf; text-decoration: none;">

assembler/src/spades_pipeline/stages/spades_stage.py

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<a href="#0109eb8c8746266314fbfa66403f9a857e555a32" style="color: #1068bf; text-decoration: none;">

assembler/src/spades_pipeline/support.py

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<h4 style="margin-top: 10px; margin-bottom: 10px;">Changes:</h4>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">README.md</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -6,7 +6,7 @@</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Contributor Covenant</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg</span><span class="p">)</span>](code_of_conduct.md)</span>

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC7" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC9" class="line" lang="markdown"><span class="nt" style="color: #000080;"><font</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">20</span><span class="nt" style="color: #000080;">></span><span class="gs" style="font-weight: 600;">__SPAdes 3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span> Manual__</span><span class="nt" style="color: #000080;"></font></span></span>

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<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC9" class="line" lang="markdown"><span class="nt" style="color: #000080;"><font</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">20</span><span class="nt" style="color: #000080;">></span><span class="gs" style="font-weight: 600;">__SPAdes 3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span> Manual__</span><span class="nt" style="color: #000080;"></font></span></span>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC10" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC11" class="line" lang="markdown"><span class="p">1.</span> <span class="p">[</span><span class="nv" style="color: #008080;">About SPAdes</span><span class="p">](</span><span class="sx" style="color: #d14;">#sec1</span><span class="p">)</span> <span class="nt" style="color: #000080;"></br></span></span>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC12" class="line" lang="markdown"><span class="p">    1.</span>1. <span class="p">[</span><span class="nv" style="color: #008080;">Supported data types</span><span class="p">](</span><span class="sx" style="color: #d14;">#sec1.1</span><span class="p">)</span><span class="nt" style="color: #000080;"></br></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -42,7 +42,7 @@</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC42" class="line" lang="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec1"</span><span class="nt" style="color: #000080;">></a></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC43" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># About SPAdes</span></span>

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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC44" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC45" class="line" lang="markdown">SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. This manual will help you to install and run SPAdes. SPAdes version 3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span> was released under GPLv2 on <span class="idiff deletion" style="background-color: #fac5cd;">February 1</span>, 202<span class="idiff right deletion" style="background-color: #fac5cd;">1</span> and can be downloaded from <span class="nv" style="color: #008080;"><http://cab.spbu.ru/software/spades/></span>. </span>

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<td class="old_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC45" class="line" lang="markdown">SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. This manual will help you to install and run SPAdes. SPAdes version 3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span> was released under GPLv2 on <span class="idiff addition" style="background-color: #c7f0d2;">July 14th</span>, 202<span class="idiff right addition" style="background-color: #c7f0d2;">2</span> and can be downloaded from <span class="nv" style="color: #008080;"><http://cab.spbu.ru/software/spades/></span>. </span>

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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC46" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC47" class="line" lang="markdown">The latest SPAdes paper describing various pipelines in a protocol format is available <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.102</span><span class="p">)</span>.</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC48" class="line" lang="markdown"></span>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -51,11 +51,11 @@ The latest SPAdes paper describing various pipelines in a protocol format is ava</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC51" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC52" class="line" lang="markdown">The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads.</span>

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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC53" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC54" class="line" lang="markdown">Version 3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span> of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.</span>

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<td class="old_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC54" class="line" lang="markdown">Version 3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span> of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC55" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC56" class="line" lang="markdown">If you have high-coverage data for bacterial/viral isolate or multi-cell organism, we highly recommend to use <span class="p">[</span><span class="nv" style="color: #008080;">`--isolate`</span><span class="p">](</span><span class="sx" style="color: #d14;">#isolate</span><span class="p">)</span> option.</span>

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<td class="old_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC57" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC58" class="line" lang="markdown">SPAdes 3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span> includes the following additional pipelines:</span>

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<td class="old_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC58" class="line" lang="markdown">SPAdes 3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span> includes the following additional pipelines:</span>

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<td class="new_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC59" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC60" class="line" lang="markdown"><span class="p">-</span>   metaSPAdes - a pipeline for metagenomic data sets (see <span class="p">[</span><span class="nv" style="color: #008080;">metaSPAdes options</span><span class="p">](</span><span class="sx" style="color: #d14;">#meta</span><span class="p">)</span>).</span>

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<td class="old_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC61" class="line" lang="markdown"><span class="p">-</span>   plasmidSPAdes - a pipeline for extracting and assembling plasmids from WGS data sets (see <span class="p">[</span><span class="nv" style="color: #008080;">plasmid options</span><span class="p">](</span><span class="sx" style="color: #d14;">#plasmid</span><span class="p">)</span>).</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -187,13 +187,13 @@ In case of successful installation the following files will be placed in the `bi</td>

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<td class="new_line diff-line-num" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC187" class="line" lang="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec2.1"</span><span class="nt" style="color: #000080;">></a></span></span>

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<td class="old_line diff-line-num" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC188" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Downloading SPAdes Linux binaries</span></span>

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<td class="old_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC189" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC190" class="line" lang="markdown">To download <span class="p">[</span><span class="nv" style="color: #008080;">SPAdes Linux binaries</span><span class="p">](</span><span class="sx" style="color: #d14;">http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>-Linux.tar.gz</span><span class="p">)</span> and extract them, go to the directory in which you wish SPAdes to be installed and run:</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC190" class="line" lang="markdown">To download <span class="p">[</span><span class="nv" style="color: #008080;">SPAdes Linux binaries</span><span class="p">](</span><span class="sx" style="color: #d14;">http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>-Linux.tar.gz</span><span class="p">)</span> and extract them, go to the directory in which you wish SPAdes to be installed and run:</span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC191" class="line" lang="markdown"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC192" class="line" lang="markdown"><span class="p">```</span><span class="nl"> bash</span></span>

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<td class="old_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

193

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<td class="new_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

193

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC193" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

194

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<td class="new_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC194" class="line" lang="markdown">    wget http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>-Linux.tar.gz</span>

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<td class="old_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

195

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<td class="new_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC195" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzf</span> SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>-Linux.tar.gz</span>

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<td class="old_line diff-line-num old" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

196

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<td class="new_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC196" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">cd </span>SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>-Linux/bin/</span>

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<td class="old_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

194

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC194" class="line" lang="markdown">    wget http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>-Linux.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

195

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC195" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzf</span> SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>-Linux.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

196

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC196" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">cd </span>SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>-Linux/bin/</span>

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<td class="old_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

197

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<td class="new_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

197

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC197" class="line" lang="markdown"><span class="p">```</span></span>

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<td class="old_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

198

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<td class="new_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

198

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC198" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

199

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<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

199

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC199" class="line" lang="markdown">In this case you do not need to run any installation scripts - SPAdes is ready to use. We also suggest adding SPAdes installation directory to the <span class="sb" style="color: #d14;">`PATH`</span> variable. <span class="p">[](</span><span class="sx" style="color: #d14;">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -203,13 +203,13 @@ Note, that pre-build binaries do not work on new Linux kernels.</td>

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<td class="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC203" class="line" lang="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec2.2"</span><span class="nt" style="color: #000080;">></a></span></span>

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<td class="old_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC204" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Downloading SPAdes binaries for Mac</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC205" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC206" class="line" lang="markdown">To obtain <span class="p">[</span><span class="nv" style="color: #008080;">SPAdes binaries for Mac</span><span class="p">](</span><span class="sx" style="color: #d14;">http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>-Darwin.tar.gz</span><span class="p">)</span>, go to the directory in which you wish SPAdes to be installed and run:</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

206

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC206" class="line" lang="markdown">To obtain <span class="p">[</span><span class="nv" style="color: #008080;">SPAdes binaries for Mac</span><span class="p">](</span><span class="sx" style="color: #d14;">http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>-Darwin.tar.gz</span><span class="p">)</span>, go to the directory in which you wish SPAdes to be installed and run:</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

207

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<td class="new_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

207

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC207" class="line" lang="markdown"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

208

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<td class="new_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

208

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC208" class="line" lang="markdown"><span class="p">```</span><span class="nl"> bash</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

209

</td>

<td class="new_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

209

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC209" class="line" lang="markdown"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

210

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<td class="new_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC210" class="line" lang="markdown">    curl http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff deletion" style="background-color: #fac5cd;">4</span>-Darwin.tar.gz <span class="nt" style="color: #000080;">-o</span> SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>-Darwin.tar.gz</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

211

</td>

<td class="new_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC211" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-zxf</span> SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>-Darwin.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

212

</td>

<td class="new_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC212" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">cd </span>SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>-Darwin/bin/</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

210

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC210" class="line" lang="markdown">    curl http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff addition" style="background-color: #c7f0d2;">5</span>-Darwin.tar.gz <span class="nt" style="color: #000080;">-o</span> SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>-Darwin.tar.gz</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

211

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC211" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-zxf</span> SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>-Darwin.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

212

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC212" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">cd </span>SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>-Darwin/bin/</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

213

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<td class="new_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

213

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC213" class="line" lang="markdown"><span class="p">```</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

214

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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

214

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC214" class="line" lang="markdown"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

215

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<td class="new_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

215

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC215" class="line" lang="markdown">Just as in Linux, SPAdes is ready to use and no further installation steps are required. We also suggest adding SPAdes installation directory to the <span class="sb" style="color: #d14;">`PATH`</span> variable. <span class="p">[](</span><span class="sx" style="color: #d14;">)</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -224,13 +224,13 @@ If you wish to compile SPAdes by yourself you will need the following libraries</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC224" class="line" lang="markdown"><span class="p">-</span>   zlib</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC225" class="line" lang="markdown"><span class="p">-</span>   libbz2</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC226" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC227" class="line" lang="markdown">If you meet these requirements, you can download the <span class="p">[</span><span class="nv" style="color: #008080;">SPAdes source code</span><span class="p">](</span><span class="sx" style="color: #d14;">http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>.tar.gz</span><span class="p">)</span>:</span>

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<td class="old_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC227" class="line" lang="markdown">If you meet these requirements, you can download the <span class="p">[</span><span class="nv" style="color: #008080;">SPAdes source code</span><span class="p">](</span><span class="sx" style="color: #d14;">http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>.tar.gz</span><span class="p">)</span>:</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC228" class="line" lang="markdown"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC229" class="line" lang="markdown"><span class="p">```</span><span class="nl"> bash</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC230" class="line" lang="markdown"></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC231" class="line" lang="markdown">    wget http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>.tar.gz</span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC232" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzf</span> SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>.tar.gz</span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC233" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">cd </span>SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC231" class="line" lang="markdown">    wget http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>.tar.gz</span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC232" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzf</span> SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>.tar.gz</span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC233" class="line" lang="markdown">    <span class="nb" style="color: #0086b3;">cd </span>SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC234" class="line" lang="markdown"><span class="p">```</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC235" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC236" class="line" lang="markdown">and build it with the following script:</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -309,7 +309,7 @@ Thank you for using SPAdes!</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC309" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC310" class="line" lang="markdown">SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.</span>

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<td class="new_line diff-line-num" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC311" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC312" class="line" lang="markdown">To run SPAdes 3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span> you need at least one library of the following types:</span>

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<td class="old_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC312" class="line" lang="markdown">To run SPAdes 3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span> you need at least one library of the following types:</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC313" class="line" lang="markdown"></span>

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<td class="new_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC314" class="line" lang="markdown"><span class="p">-</span>   Illumina paired-end/high-quality mate-pairs/unpaired reads</span>

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<td class="old_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC315" class="line" lang="markdown"><span class="p">-</span>   IonTorrent paired-end/high-quality mate-pairs/unpaired reads</span>

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<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#ae55101b54ce2616006582a65f21f81a27f56ef0" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/VERSION</strong></a>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1" class="line" lang="plaintext">3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span></span></pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1" class="line" lang="plaintext">3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span></span></pre></td>

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<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#a9849095d161d6172a4b8c397180ac07a1c37ec4" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/changelog.html</strong></a>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3,6 +3,15 @@</td>

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3

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" class="line" lang="html"></span>

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4

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

4

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>SPAdes Genome Assembler changelog<span class="nt" style="color: #000080;"></h2></span></span>

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5

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

5

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="html"></span>

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<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="html"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC7" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>SPAdes 3.15.5, 14 July 2022<span class="nt" style="color: #000080;"></h3></span></span>

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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC8" class="line" lang="html"></span>

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<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC9" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>NEW: Support DNA HMMs. <span class="nt" style="color: #000080;"><p></span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC10" class="line" lang="html"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC11" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>FIX: use-after-free in PB aligner. <span class="nt" style="color: #000080;"><p></span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC12" class="line" lang="html"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC13" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>FIX: duplicated sequences in metaplasmid / metaviral mode. <span class="nt" style="color: #000080;"><p></span></span>

</pre></td>

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14

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC14" class="line" lang="html"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

6

</td>

<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

15

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC15" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>SPAdes 3.15.4, 1 February 2022<span class="nt" style="color: #000080;"></h3></span></span>

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7

</td>

<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

16

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC16" class="line" lang="html"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

8

</td>

<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

17

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC17" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>FIX: MacOS Monterey memory limit failure. <span class="nt" style="color: #000080;"><p></span></span>

</pre></td>

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1

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1" class="line" lang="html"><span class="nt" style="color: #000080;"><html></span>     <span class="nt" style="color: #000080;"><head></span>         <span class="nt" style="color: #000080;"><title></span>SPAdes 3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span> Manual<span class="nt" style="color: #000080;"></title></span>         <span class="nt" style="color: #000080;"><style </span><span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text/css"</span><span class="nt" style="color: #000080;">></span>             <span class="nc" style="color: #458; font-weight: 600;">.highlight</span>  <span class="nt" style="color: #000080;">pre</span> <span class="p">{</span>               <span class="nl">background-color</span><span class="p">:</span> <span class="m" style="color: #099;">#f0f2f4</span><span class="p">;</span>               <span class="nl">border-radius</span><span class="p">:</span> <span class="m" style="color: #099;">2px</span><span class="p">;</span>               <span class="nl">font-size</span><span class="p">:</span> <span class="m" style="color: #099;">100%</span><span class="p">;</span>               <span class="nl">line-height</span><span class="p">:</span> <span class="m" style="color: #099;">1.45</span><span class="p">;</span>               <span class="nl">overflow</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">auto</span><span class="p">;</span>               <span class="nl">padding</span><span class="p">:</span> <span class="m" style="color: #099;">16px</span><span class="p">;</span>             <span class="p">}</span>         <span class="nt" style="color: #000080;"></style></span>     <span class="nt" style="color: #000080;"></head></span>     <span class="nt" style="color: #000080;"><body><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://chihua.cab.spbu.ru:3000/buildConfiguration/SPAdesBasicTests_RunAll?mode=builds"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://camo.githubusercontent.com/21b928ad15b5735360cb555da4951c8dee2ef5633fd61c3fce22bb157f9dc1c5/687474703a2f2f6368696875612e6361622e737062752e72753a333030302f6170702f726573742f6275696c64732f6275696c64547970653a2869643a535041646573426173696354657374735f52756e416c6c292f73746174757349636f6e"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"TeamCity Simple Build Status"</span> <span class="na" style="color: #008080;">data-canonical-src=</span><span class="s" style="color: #d14;">"http://chihua.cab.spbu.ru:3000/app/rest/builds/buildType:(id:SPAdesBasicTests_RunAll)/statusIcon"</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"max-width: 100%;"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1" class="line" lang="html"><span class="nt" style="color: #000080;"><html></span>     <span class="nt" style="color: #000080;"><head></span>         <span class="nt" style="color: #000080;"><title></span>SPAdes 3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span> Manual<span class="nt" style="color: #000080;"></title></span>         <span class="nt" style="color: #000080;"><style </span><span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text/css"</span><span class="nt" style="color: #000080;">></span>             <span class="nc" style="color: #458; font-weight: 600;">.highlight</span>  <span class="nt" style="color: #000080;">pre</span> <span class="p">{</span>               <span class="nl">background-color</span><span class="p">:</span> <span class="m" style="color: #099;">#f0f2f4</span><span class="p">;</span>               <span class="nl">border-radius</span><span class="p">:</span> <span class="m" style="color: #099;">2px</span><span class="p">;</span>               <span class="nl">font-size</span><span class="p">:</span> <span class="m" style="color: #099;">100%</span><span class="p">;</span>               <span class="nl">line-height</span><span class="p">:</span> <span class="m" style="color: #099;">1.45</span><span class="p">;</span>               <span class="nl">overflow</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">auto</span><span class="p">;</span>               <span class="nl">padding</span><span class="p">:</span> <span class="m" style="color: #099;">16px</span><span class="p">;</span>             <span class="p">}</span>         <span class="nt" style="color: #000080;"></style></span>     <span class="nt" style="color: #000080;"></head></span>     <span class="nt" style="color: #000080;"><body><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://chihua.cab.spbu.ru:3000/buildConfiguration/SPAdesBasicTests_RunAll?mode=builds"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://camo.githubusercontent.com/21b928ad15b5735360cb555da4951c8dee2ef5633fd61c3fce22bb157f9dc1c5/687474703a2f2f6368696875612e6361622e737062752e72753a333030302f6170702f726573742f6275696c64732f6275696c64547970653a2869643a535041646573426173696354657374735f52756e416c6c292f73746174757349636f6e"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"TeamCity Simple Build Status"</span> <span class="na" style="color: #008080;">data-canonical-src=</span><span class="s" style="color: #d14;">"http://chihua.cab.spbu.ru:3000/app/rest/builds/buildType:(id:SPAdesBasicTests_RunAll)/statusIcon"</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"max-width: 100%;"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://www.gnu.org/licenses/old-licenses/gpl-2.0"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://camo.githubusercontent.com/c76156a44047d8a6b64fc1fa16118996c422cff2959c1ae82127260b29e990ef/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f6c6963656e63652d47504c76322d626c7565"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"License"</span> <span class="na" style="color: #008080;">data-canonical-src=</span><span class="s" style="color: #d14;">"https://img.shields.io/badge/licence-GPLv2-blue"</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"max-width: 100%;"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

3

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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/ablab/spades/releases/"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://camo.githubusercontent.com/b67a7145a28ab5560f54b811c18353c4771fa5ae62a344f4d5e53a4c0a9da5b4/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f762f72656c656173652f61626c61622f737061646573"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"GitHub release (latest by date)"</span> <span class="na" style="color: #008080;">data-canonical-src=</span><span class="s" style="color: #d14;">"https://img.shields.io/github/v/release/ablab/spades"</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"max-width: 100%;"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

4

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/ablab/spades/releases"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://camo.githubusercontent.com/a8ba4fbdefabcc61b7a4d41a40fb19c92e96d49717bd24414252a4f460a34f09/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f646f776e6c6f6164732f61626c61622f7370616465732f746f74616c2e7376673f7374796c653d736f6369616c266c6f676f3d676974687562266c6162656c3d446f776e6c6f6164"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"GitHub Downloads"</span> <span class="na" style="color: #008080;">data-canonical-src=</span><span class="s" style="color: #d14;">"https://img.shields.io/github/downloads/ablab/spades/total.svg?style=social&amp;logo=github&amp;label=Download"</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"max-width: 100%;"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

5

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

5

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://anaconda.org/bioconda/spades"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://camo.githubusercontent.com/24a3286de783bcb188f9e010b910a26db4026ecf4b05f184fb3f71f4892f6c77/68747470733a2f2f616e61636f6e64612e6f72672f62696f636f6e64612f7370616465732f6261646765732f646f776e6c6f6164732e737667"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"BioConda Downloads"</span> <span class="na" style="color: #008080;">data-canonical-src=</span><span class="s" style="color: #d14;">"https://anaconda.org/bioconda/spades/badges/downloads.svg"</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"max-width: 100%;"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC6" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"code_of_conduct.md"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://camo.githubusercontent.com/9a5e1f5558bc77986d831a81a6f80819da5a94c13d3aca339a0993119f535a06/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f436f6e7472696275746f72253230436f76656e616e742d322e302d3462616161612e737667"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"Contributor Covenant"</span> <span class="na" style="color: #008080;">data-canonical-src=</span><span class="s" style="color: #d14;">"https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg"</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"max-width: 100%;"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC7" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><strong></span>SPAdes 3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span> Manual<span class="nt" style="color: #000080;"></strong></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC7" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><strong></span>SPAdes 3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span> Manual<span class="nt" style="color: #000080;"></strong></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="html"><span class="nt" style="color: #000080;"><ol</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec1"</span><span class="nt" style="color: #000080;">></span>About SPAdes<span class="nt" style="color: #000080;"></a></span> <span class="nt" style="color: #000080;"><br></span></span>

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC10" class="line" lang="html">1.1. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec1.1"</span><span class="nt" style="color: #000080;">></span>Supported data types<span class="nt" style="color: #000080;"></a><br></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC39" class="line" lang="html"><span class="nt" style="color: #000080;"></ol></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC40" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec1"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC41" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>About SPAdes<span class="nt" style="color: #000080;"></h1></span></span>

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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC42" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. This manual will help you to install and run SPAdes. SPAdes version 3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span> was released under GPLv2 on <span class="idiff deletion" style="background-color: #fac5cd;">February 1</span>, 202<span class="idiff right deletion" style="background-color: #fac5cd;">1</span> and can be downloaded from <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://cab.spbu.ru/software/spades/"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>http://cab.spbu.ru/software/spades/<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC42" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. This manual will help you to install and run SPAdes. SPAdes version 3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span> was released under GPLv2 on <span class="idiff addition" style="background-color: #c7f0d2;">July 14th</span>, 202<span class="idiff right addition" style="background-color: #c7f0d2;">2</span> and can be downloaded from <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://cab.spbu.ru/software/spades/"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>http://cab.spbu.ru/software/spades/<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC43" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The latest SPAdes paper describing various pipelines in a protocol format is available <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.102"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC44" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec1.1"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC45" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Supported data types<span class="nt" style="color: #000080;"></h2></span></span>

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<td class="old_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC46" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC47" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Version 3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span> of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC48" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>If you have high-coverage data for bacterial/viral isolate or multi-cell organism, we highly recommend to use <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#isolate"</span><span class="nt" style="color: #000080;">><code></span>--isolate<span class="nt" style="color: #000080;"></code></a></span> option.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC49" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes 3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span> includes the following additional pipelines:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC47" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Version 3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span> of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC48" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>If you have high-coverage data for bacterial/viral isolate or multi-cell organism, we highly recommend to use <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#isolate"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--isolate<span class="nt" style="color: #000080;"></code></a></span> option.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC49" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes 3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span> includes the following additional pipelines:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC50" class="line" lang="html"><span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC51" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>metaSPAdes - a pipeline for metagenomic data sets (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#meta"</span><span class="nt" style="color: #000080;">></span>metaSPAdes options<span class="nt" style="color: #000080;"></a></span>).<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC52" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>plasmidSPAdes - a pipeline for extracting and assembling plasmids from WGS data sets (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#plasmid"</span><span class="nt" style="color: #000080;">></span>plasmid options<span class="nt" style="color: #000080;"></a></span>).<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -57,7 +57,7 @@</td>

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<td class="old_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC57" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>coronaSPAdes is a special mode of rnaviralSPAdes specifically aimed for SARS-CoV-2 <span class="nt" style="color: #000080;"><em></span>de novo<span class="nt" style="color: #000080;"></em></span> assembly.<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC58" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>truSPAdes - (DEPRECATED) a module for TruSeq barcode assembly (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"truspades_manual.html"</span><span class="nt" style="color: #000080;">></span>truSPAdes manual<span class="nt" style="color: #000080;"></a></span>).<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC59" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC60" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In addition, we provide several stand-alone binaries with relatively simple command-line interface: <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec4.1"</span><span class="nt" style="color: #000080;">></span>k-mer counting<span class="nt" style="color: #000080;"></a></span> (<span class="nt" style="color: #000080;"><code></span>spades-kmercounter<span class="nt" style="color: #000080;"></code></span>), <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec4.2"</span><span class="nt" style="color: #000080;">></span>assembly graph construction<span class="nt" style="color: #000080;"></a></span> (<span class="nt" style="color: #000080;"><code></span>spades-gbuilder<span class="nt" style="color: #000080;"></code></span>) and <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec4.3"</span><span class="nt" style="color: #000080;">></span>long read to graph aligner<span class="nt" style="color: #000080;"></a></span> (<span class="nt" style="color: #000080;"><code></span>spades-gmapper<span class="nt" style="color: #000080;"></code></span>). To learn options of these tools you can either run them without any parameters or read <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec4"</span><span class="nt" style="color: #000080;">></span>this section<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC60" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In addition, we provide several stand-alone binaries with relatively simple command-line interface: <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec4.1"</span><span class="nt" style="color: #000080;">></span>k-mer counting<span class="nt" style="color: #000080;"></a></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-kmercounter<span class="nt" style="color: #000080;"></code></span>), <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec4.2"</span><span class="nt" style="color: #000080;">></span>assembly graph construction<span class="nt" style="color: #000080;"></a></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-gbuilder<span class="nt" style="color: #000080;"></code></span>) and <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec4.3"</span><span class="nt" style="color: #000080;">></span>long read to graph aligner<span class="nt" style="color: #000080;"></a></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-gmapper<span class="nt" style="color: #000080;"></code></span>). To learn options of these tools you can either run them without any parameters or read <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec4"</span><span class="nt" style="color: #000080;">></span>this section<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC61" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC62" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec1.2"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC63" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes pipeline<span class="nt" style="color: #000080;"></h2></span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC139" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec2"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC140" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Installation<span class="nt" style="color: #000080;"></h1></span></span>

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<td class="old_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC141" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes requires a 64-bit Linux system or Mac OS and Python (supported versions are Python 2.7, and Python3: 3.2 and higher) to be pre-installed on it. To obtain SPAdes you can either download binaries or download source code and compile it yourself. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC142" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In case of successful installation the following files will be placed in the <span class="nt" style="color: #000080;"><code></span>bin<span class="nt" style="color: #000080;"></code></span> directory:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

142

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC142" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In case of successful installation the following files will be placed in the <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>bin<span class="nt" style="color: #000080;"></code></span> directory:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

143

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<td class="new_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC143" class="line" lang="html"><span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="old_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

144

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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC144" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>spades.py<span class="nt" style="color: #000080;"></code></span> (main executable script)<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

145

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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC145" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>metaspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#meta"</span><span class="nt" style="color: #000080;">></span>metaSPAdes<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

146

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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC146" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>plasmidspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#plasmid"</span><span class="nt" style="color: #000080;">></span>plasmidSPAdes<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC147" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>metaplasmidspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#metaextrachromosomal"</span><span class="nt" style="color: #000080;">></span>metaplasmidSPAdes<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC148" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>metaviralspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#metaextrachromosomal"</span><span class="nt" style="color: #000080;">></span>metaviralSPAdes<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

149

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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC149" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>rnaspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"rnaspades_manual.html"</span><span class="nt" style="color: #000080;">></span>rnaSPAdes<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

150

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC150" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>truspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"truspades_manual.html"</span><span class="nt" style="color: #000080;">></span>truSPAdes<span class="nt" style="color: #000080;"></a></span>, DEPRECATED)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

151

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC151" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>rnaviralspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for rnaviralSPAdes)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

152

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC152" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>coronaspades.py<span class="nt" style="color: #000080;"></code></span> (wrapper script for coronaSPAdes mode)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

153

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC153" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>spades-core<span class="nt" style="color: #000080;"></code></span>  (assembly module)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

154

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC154" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>spades-gbuilder<span class="nt" style="color: #000080;"></code></span>  (standalone graph builder application)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

155

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC155" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>spades-gmapper<span class="nt" style="color: #000080;"></code></span>  (standalone long read to graph aligner)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

156

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC156" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>spades-kmercount<span class="nt" style="color: #000080;"></code></span>  (standalone k-mer counting application)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

157

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC157" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>spades-hammer<span class="nt" style="color: #000080;"></code></span>  (read error correcting module for Illumina reads)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

158

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC158" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>spades-ionhammer<span class="nt" style="color: #000080;"></code></span>  (read error correcting module for IonTorrent reads)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

159

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC159" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>spades-bwa<span class="nt" style="color: #000080;"></code></span>  (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://bio-bwa.sourceforge.net"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>BWA<span class="nt" style="color: #000080;"></a></span> alignment module which is required for mismatch correction)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

160

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC160" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>spades-corrector-core<span class="nt" style="color: #000080;"></code></span>  (mismatch correction module)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

161

</td>

<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC161" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>spades-truseq-scfcorrection<span class="nt" style="color: #000080;"></code></span>  (executable used in truSPAdes pipeline)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

144

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC144" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades.py<span class="nt" style="color: #000080;"></code></span> (main executable script)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

145

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC145" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>metaspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#meta"</span><span class="nt" style="color: #000080;">></span>metaSPAdes<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

146

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC146" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>plasmidspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#plasmid"</span><span class="nt" style="color: #000080;">></span>plasmidSPAdes<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

147

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC147" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>metaplasmidspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#metaextrachromosomal"</span><span class="nt" style="color: #000080;">></span>metaplasmidSPAdes<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

148

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC148" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>metaviralspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#metaextrachromosomal"</span><span class="nt" style="color: #000080;">></span>metaviralSPAdes<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

149

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC149" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>rnaspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"rnaspades_manual.html"</span><span class="nt" style="color: #000080;">></span>rnaSPAdes<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

150

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC150" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>truspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"truspades_manual.html"</span><span class="nt" style="color: #000080;">></span>truSPAdes<span class="nt" style="color: #000080;"></a></span>, DEPRECATED)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

151

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC151" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>rnaviralspades.py<span class="nt" style="color: #000080;"></code></span> (main executable script for rnaviralSPAdes)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC152" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>coronaspades.py<span class="nt" style="color: #000080;"></code></span> (wrapper script for coronaSPAdes mode)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

153

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC153" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-core<span class="nt" style="color: #000080;"></code></span>  (assembly module)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

154

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC154" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-gbuilder<span class="nt" style="color: #000080;"></code></span>  (standalone graph builder application)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

155

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC155" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-gmapper<span class="nt" style="color: #000080;"></code></span>  (standalone long read to graph aligner)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

156

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC156" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-kmercount<span class="nt" style="color: #000080;"></code></span>  (standalone k-mer counting application)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

157

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC157" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-hammer<span class="nt" style="color: #000080;"></code></span>  (read error correcting module for Illumina reads)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

158

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC158" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-ionhammer<span class="nt" style="color: #000080;"></code></span>  (read error correcting module for IonTorrent reads)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

159

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC159" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-bwa<span class="nt" style="color: #000080;"></code></span>  (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://bio-bwa.sourceforge.net"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>BWA<span class="nt" style="color: #000080;"></a></span> alignment module which is required for mismatch correction)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

160

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC160" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-corrector-core<span class="nt" style="color: #000080;"></code></span>  (mismatch correction module)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

161

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC161" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-truseq-scfcorrection<span class="nt" style="color: #000080;"></code></span>  (executable used in truSPAdes pipeline)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

162

</td>

<td class="new_line diff-line-num" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

162

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC162" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>

</pre></td>

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163

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<td class="new_line diff-line-num" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

163

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC163" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec2.1"</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

164

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<td class="new_line diff-line-num" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

164

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC164" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Downloading SPAdes Linux binaries<span class="nt" style="color: #000080;"></h2></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

165

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<td class="new_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC165" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To download <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>-Linux.tar.gz"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>SPAdes Linux binaries<span class="nt" style="color: #000080;"></a></span> and extract them, go to the directory in which you wish SPAdes to be installed and run:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

166

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<td class="new_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC166" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    wget http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>-Linux.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

167

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<td class="new_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC167" class="line" lang="html">    tar -xzf SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>-Linux.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

168

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<td class="new_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC168" class="line" lang="html">    <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-c1"</span><span class="nt" style="color: #000080;">></span>cd<span class="nt" style="color: #000080;"></span></span> SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>-Linux/bin/<span class="nt" style="color: #000080;"></pre></div></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

169

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<td class="new_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC169" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In this case you do not need to run any installation scripts - SPAdes is ready to use. We also suggest adding SPAdes installation directory to the <span class="nt" style="color: #000080;"><code></span>PATH<span class="nt" style="color: #000080;"></code></span> variable. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

165

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC165" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To download <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>-Linux.tar.gz"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>SPAdes Linux binaries<span class="nt" style="color: #000080;"></a></span> and extract them, go to the directory in which you wish SPAdes to be installed and run:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

166

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC166" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    wget http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>-Linux.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC167" class="line" lang="html">    tar -xzf SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>-Linux.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC168" class="line" lang="html">    <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-c1"</span><span class="nt" style="color: #000080;">></span>cd<span class="nt" style="color: #000080;"></span></span> SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>-Linux/bin/<span class="nt" style="color: #000080;"></pre></div></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

169

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC169" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In this case you do not need to run any installation scripts - SPAdes is ready to use. We also suggest adding SPAdes installation directory to the <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>PATH<span class="nt" style="color: #000080;"></code></span> variable. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC170" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Note, that pre-build binaries do not work on new Linux kernels.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC171" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec2.2"</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

172

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<td class="new_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

172

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC172" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Downloading SPAdes binaries for Mac<span class="nt" style="color: #000080;"></h2></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

173

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<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC173" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To obtain <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>-Darwin.tar.gz"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>SPAdes binaries for Mac<span class="nt" style="color: #000080;"></a></span>, go to the directory in which you wish SPAdes to be installed and run:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

174

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<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC174" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    curl http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff deletion" style="background-color: #fac5cd;">4</span>-Darwin.tar.gz -o SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>-Darwin.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

175

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<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC175" class="line" lang="html">    tar -zxf SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>-Darwin.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

176

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<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC176" class="line" lang="html">    <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-c1"</span><span class="nt" style="color: #000080;">></span>cd<span class="nt" style="color: #000080;"></span></span> SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>-Darwin/bin/<span class="nt" style="color: #000080;"></pre></div></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

177

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<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC177" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Just as in Linux, SPAdes is ready to use and no further installation steps are required. We also suggest adding SPAdes installation directory to the <span class="nt" style="color: #000080;"><code></span>PATH<span class="nt" style="color: #000080;"></code></span> variable. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

173

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC173" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To obtain <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>-Darwin.tar.gz"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>SPAdes binaries for Mac<span class="nt" style="color: #000080;"></a></span>, go to the directory in which you wish SPAdes to be installed and run:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

174

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC174" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    curl http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff addition" style="background-color: #c7f0d2;">5</span>-Darwin.tar.gz -o SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>-Darwin.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC175" class="line" lang="html">    tar -zxf SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>-Darwin.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC176" class="line" lang="html">    <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-c1"</span><span class="nt" style="color: #000080;">></span>cd<span class="nt" style="color: #000080;"></span></span> SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>-Darwin/bin/<span class="nt" style="color: #000080;"></pre></div></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC177" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Just as in Linux, SPAdes is ready to use and no further installation steps are required. We also suggest adding SPAdes installation directory to the <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>PATH<span class="nt" style="color: #000080;"></code></span> variable. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC178" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec2.3"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC179" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Downloading and compiling SPAdes source code<span class="nt" style="color: #000080;"></h2></span></span>

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<td class="old_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC180" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>If you wish to compile SPAdes by yourself you will need the following libraries to be pre-installed:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC184" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>zlib<span class="nt" style="color: #000080;"></li></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC185" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>libbz2<span class="nt" style="color: #000080;"></li></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC186" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>

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<td class="old_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC187" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>If you meet these requirements, you can download the <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>.tar.gz"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>SPAdes source code<span class="nt" style="color: #000080;"></a></span>:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC188" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    wget http://cab.spbu.ru/files/release3.15.<span class="idiff left deletion" style="background-color: #fac5cd;">4</span>/SPAdes-3.15.<span class="idiff right deletion" style="background-color: #fac5cd;">4</span>.tar.gz</span>

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<td class="new_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC189" class="line" lang="html">    tar -xzf SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>.tar.gz</span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC190" class="line" lang="html">    <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-c1"</span><span class="nt" style="color: #000080;">></span>cd<span class="nt" style="color: #000080;"></span></span> SPAdes-3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span><span class="nt" style="color: #000080;"></pre></div></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC187" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>If you meet these requirements, you can download the <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>.tar.gz"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>SPAdes source code<span class="nt" style="color: #000080;"></a></span>:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

188

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC188" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    wget http://cab.spbu.ru/files/release3.15.<span class="idiff left addition" style="background-color: #c7f0d2;">5</span>/SPAdes-3.15.<span class="idiff right addition" style="background-color: #c7f0d2;">5</span>.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

189

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC189" class="line" lang="html">    tar -xzf SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>.tar.gz</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

190

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC190" class="line" lang="html">    <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-c1"</span><span class="nt" style="color: #000080;">></span>cd<span class="nt" style="color: #000080;"></span></span> SPAdes-3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span><span class="nt" style="color: #000080;"></pre></div></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

191

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<td class="new_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

191

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC191" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>and build it with the following script:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

192

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<td class="new_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

192

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC192" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    ./spades_compile.sh<span class="nt" style="color: #000080;"></pre></div></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

193

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<td class="new_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC193" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes will be built in the directory <span class="nt" style="color: #000080;"><code></span>./bin<span class="nt" style="color: #000080;"></code></span>. If you wish to install SPAdes into another directory, you can specify full path of destination folder by running the following command in <span class="nt" style="color: #000080;"><code></span>bash<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code></span>sh<span class="nt" style="color: #000080;"></code></span>:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

193

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC193" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes will be built in the directory <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>./bin<span class="nt" style="color: #000080;"></code></span>. If you wish to install SPAdes into another directory, you can specify full path of destination folder by running the following command in <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>bash<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>sh<span class="nt" style="color: #000080;"></code></span>:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

194

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<td class="new_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

194

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC194" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    PREFIX=<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-k"</span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span><span class="nt" style="color: #000080;"></span></span>destination_dir<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-k"</span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></span></span> ./spades_compile.sh<span class="nt" style="color: #000080;"></pre></div></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

195

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<td class="new_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

195

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC195" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>for example:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

196

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<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

196

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC196" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    PREFIX=/usr/local ./spades_compile.sh<span class="nt" style="color: #000080;"></pre></div></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

197

</td>

<td class="new_line diff-line-num old" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC197" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>which will install SPAdes into <span class="nt" style="color: #000080;"><code></span>/usr/local/bin<span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

198

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<td class="new_line diff-line-num old" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC198" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>After installation you will get the same files (listed above) in <span class="nt" style="color: #000080;"><code></span>./bin<span class="nt" style="color: #000080;"></code></span> directory (or <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>destination_dir<span class="ni" style="color: #800080;">&gt;</span>/bin<span class="nt" style="color: #000080;"></code></span> if you specified PREFIX). We also suggest adding <span class="nt" style="color: #000080;"><code></span>bin<span class="nt" style="color: #000080;"></code></span> directory to the <span class="nt" style="color: #000080;"><code></span>PATH<span class="nt" style="color: #000080;"></code></span> variable. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

197

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC197" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>which will install SPAdes into <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>/usr/local/bin<span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

198

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC198" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>After installation you will get the same files (listed above) in <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>./bin<span class="nt" style="color: #000080;"></code></span> directory (or <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>destination_dir<span class="ni" style="color: #800080;">&gt;</span>/bin<span class="nt" style="color: #000080;"></code></span> if you specified PREFIX). We also suggest adding <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>bin<span class="nt" style="color: #000080;"></code></span> directory to the <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>PATH<span class="nt" style="color: #000080;"></code></span> variable. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

199

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<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

199

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC199" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec2.4"</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

200

</td>

<td class="new_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

200

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC200" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Verifying your installation<span class="nt" style="color: #000080;"></h2></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

201

</td>

<td class="new_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

201

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC201" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For testing purposes, SPAdes comes with a toy data set (reads that align to first 1000 bp of <span class="nt" style="color: #000080;"><em></span>E. coli<span class="nt" style="color: #000080;"></em></span>). To try SPAdes on this data set, run:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

202

</td>

<td class="new_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

202

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC202" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-k"</span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span><span class="nt" style="color: #000080;"></span></span>spades installation dir<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-k"</span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></span></span>/bin/spades.py --test<span class="nt" style="color: #000080;"></pre></div></span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

203

</td>

<td class="new_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC203" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>If you added <span class="nt" style="color: #000080;"><code></span>bin<span class="nt" style="color: #000080;"></code></span> folder from SPAdes installation directory to the <span class="nt" style="color: #000080;"><code></span>PATH<span class="nt" style="color: #000080;"></code></span> variable, you can run:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

203

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC203" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>If you added <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>bin<span class="nt" style="color: #000080;"></code></span> folder from SPAdes installation directory to the <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>PATH<span class="nt" style="color: #000080;"></code></span> variable, you can run:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

204

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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC205" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For the simplicity we further assume that <span class="nt" style="color: #000080;"><code></span>bin<span class="nt" style="color: #000080;"></code></span> folder from SPAdes installation directory is added to the <span class="nt" style="color: #000080;"><code></span>PATH<span class="nt" style="color: #000080;"></code></span> variable.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC205" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For the simplicity we further assume that <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>bin<span class="nt" style="color: #000080;"></code></span> folder from SPAdes installation directory is added to the <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>PATH<span class="nt" style="color: #000080;"></code></span> variable.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC206" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>If the installation is successful, you will find the following information at the end of the log:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC207" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;"><span class="idiff left right deletion" style="background-color: #fac5cd;">><code</span>></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC207" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"plain"</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">><code</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC208" class="line" lang="html">===== Assembling finished. Used k-mer sizes: 21, 33, 55</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC209" class="line" lang="html"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC210" class="line" lang="html"> * Corrected reads are in spades_test/corrected/</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -229,7 +229,7 @@ Thank you for using SPAdes!</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC229" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"input"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC230" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes input<span class="nt" style="color: #000080;"></h2></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC231" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num old" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC232" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To run SPAdes 3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span> you need at least one library of the following types:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC232" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To run SPAdes 3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span> you need at least one library of the following types:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC233" class="line" lang="html"><span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="old_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC234" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Illumina paired-end/high-quality mate-pairs/unpaired reads<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC235" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>IonTorrent paired-end/high-quality mate-pairs/unpaired reads<span class="nt" style="color: #000080;"></li></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -254,7 +254,7 @@ Thank you for using SPAdes!</td>

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<td class="old_line diff-line-num" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC254" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>In file pairs. In this case left and right reads are placed in different files and go in the same order in respective files.<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC255" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>In interleaved files. In this case, the reads are interlaced, so that each right read goes after the corresponding paired left read.<span class="nt" style="color: #000080;"></li></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC256" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>

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<td class="old_line diff-line-num old" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC257" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For example, Illumina produces paired-end reads in two files: <span class="nt" style="color: #000080;"><code></span>R1.fastq<span class="nt" style="color: #000080;"></code></span> and <span class="nt" style="color: #000080;"><code></span>R2.fastq<span class="nt" style="color: #000080;"></code></span>. If you choose to store reads in file pairs make sure that for every read from <span class="nt" style="color: #000080;"><code></span>R1.fastq<span class="nt" style="color: #000080;"></code></span> the corresponding paired read from <span class="nt" style="color: #000080;"><code></span>R2.fastq<span class="nt" style="color: #000080;"></code></span> is placed in the respective paired file on the same line number. If you choose to use interleaved files, every read from <span class="nt" style="color: #000080;"><code></span>R1.fastq<span class="nt" style="color: #000080;"></code></span> should be followed by the corresponding paired read from <span class="nt" style="color: #000080;"><code></span>R2.fastq<span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC257" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For example, Illumina produces paired-end reads in two files: <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>R1.fastq<span class="nt" style="color: #000080;"></code></span> and <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>R2.fastq<span class="nt" style="color: #000080;"></code></span>. If you choose to store reads in file pairs make sure that for every read from <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>R1.fastq<span class="nt" style="color: #000080;"></code></span> the corresponding paired read from <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>R2.fastq<span class="nt" style="color: #000080;"></code></span> is placed in the respective paired file on the same line number. If you choose to use interleaved files, every read from <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>R1.fastq<span class="nt" style="color: #000080;"></code></span> should be followed by the corresponding paired read from <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>R2.fastq<span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC258" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>If adapter and/or quality trimming software has been used prior to assembly, files with the orphan reads can be provided as "single read files" for the corresponding read-pair library.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC259" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"input:merged"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC260" class="line" lang="html">If you have merged some of the reads from your paired-end (not mate-pair or high-quality mate-pair) library (using tools s.a. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmerge-guide/"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>BBMerge<span class="nt" style="color: #000080;"></a></span> or <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://bitbucket.org/yaoornl/align_test/overview"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>STORM<span class="nt" style="color: #000080;"></a></span>), you should provide the file with resulting reads as a "merged read file" for the corresponding library.<span class="nt" style="color: #000080;"><br></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -269,44 +269,44 @@ Note that non-empty files with the remaining unmerged left/right reads (separate</td>

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<td class="new_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC269" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>PacBio and Oxford Nanopore reads<span class="nt" style="color: #000080;"></h3></span></span>

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<td class="old_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC270" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes can take as an input an unlimited number of PacBio and Oxford Nanopore libraries.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC271" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>PacBio CLR and Oxford Nanopore reads are used for hybrid assemblies (e.g. with Illumina or IonTorrent). There is no need to pre-correct this kind of data. SPAdes will use PacBio CLR and Oxford Nanopore reads for gap closure and repeat resolution.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC272" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For PacBio you just need to have filtered subreads in FASTQ/FASTA format. Provide these filtered subreads using <span class="nt" style="color: #000080;"><code></span>--pacbio<span class="nt" style="color: #000080;"></code></span> option. Oxford Nanopore reads are provided with <span class="nt" style="color: #000080;"><code></span>--nanopore<span class="nt" style="color: #000080;"></code></span> option.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC272" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For PacBio you just need to have filtered subreads in FASTQ/FASTA format. Provide these filtered subreads using <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--pacbio<span class="nt" style="color: #000080;"></code></span> option. Oxford Nanopore reads are provided with <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--nanopore<span class="nt" style="color: #000080;"></code></span> option.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC273" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>PacBio CCS/Reads of Insert reads or pre-corrected (using third-party software) PacBio CLR / Oxford Nanopore reads can be simply provided as single reads to SPAdes.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC274" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"input:contigs"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC275" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Additional contigs<span class="nt" style="color: #000080;"></h3></span></span>

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<td class="new_line diff-line-num old" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC276" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In case you have contigs of the same genome generated by other assembler(s) and you wish to merge them into SPAdes assembly, you can specify additional contigs using <span class="nt" style="color: #000080;"><code></span>--trusted-contigs<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code></span>--untrusted-contigs<span class="nt" style="color: #000080;"></code></span>. First option is used when high quality contigs are available. These contigs will be used for graph construction, gap closure and repeat resolution. Second option is used for less reliable contigs that may have more errors or contigs of unknown quality. These contigs will be used only for gap closure and repeat resolution. The number of additional contigs is unlimited.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC276" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In case you have contigs of the same genome generated by other assembler(s) and you wish to merge them into SPAdes assembly, you can specify additional contigs using <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--trusted-contigs<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--untrusted-contigs<span class="nt" style="color: #000080;"></code></span>. First option is used when high quality contigs are available. These contigs will be used for graph construction, gap closure and repeat resolution. Second option is used for less reliable contigs that may have more errors or contigs of unknown quality. These contigs will be used only for gap closure and repeat resolution. The number of additional contigs is unlimited.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC277" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Note, that SPAdes does not perform assembly using genomes of closely-related species. Only contigs of the same genome should be specified.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC278" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

279

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<td class="new_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC279" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec3.2"</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC280" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes command line options<span class="nt" style="color: #000080;"></h2></span></span>

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<td class="old_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC281" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To run SPAdes from the command line, type<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC282" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    spades.py [options] -o <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-k"</span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span><span class="nt" style="color: #000080;"></span></span>output_dir<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-k"</span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></span></pre></div></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC283" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Note that we assume that <span class="nt" style="color: #000080;"><code></span>bin<span class="nt" style="color: #000080;"></code></span> forder from SPAdes installation directory is added to the <span class="nt" style="color: #000080;"><code></span>PATH<span class="nt" style="color: #000080;"></code></span> variable (provide full path to SPAdes executable otherwise: <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>spades installation dir<span class="ni" style="color: #800080;">&gt;</span>/bin/spades.py<span class="nt" style="color: #000080;"></code></span>). <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC283" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Note that we assume that <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>bin<span class="nt" style="color: #000080;"></code></span> forder from SPAdes installation directory is added to the <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>PATH<span class="nt" style="color: #000080;"></code></span> variable (provide full path to SPAdes executable otherwise: <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>spades installation dir<span class="ni" style="color: #800080;">&gt;</span>/bin/spades.py<span class="nt" style="color: #000080;"></code></span>). <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC284" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"basicopt"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC285" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Basic options<span class="nt" style="color: #000080;"></h3></span></span>

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<td class="old_line diff-line-num old" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC286" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-o <span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC286" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-o <span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC287" class="line" lang="html">Specify the output directory. Required option.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC288" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC289" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"isolate"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC290" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>--isolate <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC290" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--isolate <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC291" class="line" lang="html">This flag is highly recommended for high-coverage isolate and multi-cell Illumina data; improves the assembly quality and running time.<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC292" class="line" lang="html">We also recommend to trim your reads prior to the assembly. More details can be found <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://cab.spbu.ru/benchmarking-tools-for-de-novo-microbial-assembly/"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC293" class="line" lang="html">This option is not compatible with <span class="nt" style="color: #000080;"><code></span>--only-error-correction<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code></span>--careful<span class="nt" style="color: #000080;"></code></span> options.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC293" class="line" lang="html">This option is not compatible with <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--only-error-correction<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--careful<span class="nt" style="color: #000080;"></code></span> options.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC294" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sc"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="new_line diff-line-num old" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC295" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>--sc <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC295" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--sc <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC296" class="line" lang="html">This flag is required for MDA (single-cell) data.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC297" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC298" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"meta"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC299" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>--meta <span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code></span>metaspades.py<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC300" class="line" lang="html">This flag is recommended when assembling metagenomic data sets (runs metaSPAdes, see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.cshlp.org/content/27/5/824.short"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>paper<span class="nt" style="color: #000080;"></a></span> for more details). Currently metaSPAdes supports only a <span class="nt" style="color: #000080;"><strong><em></span>single<span class="nt" style="color: #000080;"></em></strong></span> short-read library which has to be <span class="nt" style="color: #000080;"><strong><em></span>paired-end<span class="nt" style="color: #000080;"></em></strong></span> (we hope to remove this restriction soon). In addition, you can provide long reads (e.g. using <span class="nt" style="color: #000080;"><code></span>--pacbio<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code></span>--nanopore<span class="nt" style="color: #000080;"></code></span> options), but hybrid assembly for metagenomes remains an experimental pipeline and optimal performance is not guaranteed. It does not support <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#correctoropt"</span><span class="nt" style="color: #000080;">></span>careful mode<span class="nt" style="color: #000080;"></a></span> (mismatch correction is not available). In addition, you cannot specify coverage cutoff for metaSPAdes. Note that metaSPAdes might be very sensitive to presence of the technical sequences remaining in the data (most notably adapter readthroughs), please run quality control and pre-process your data accordingly.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC299" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--meta <span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>metaspades.py<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC300" class="line" lang="html">This flag is recommended when assembling metagenomic data sets (runs metaSPAdes, see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.cshlp.org/content/27/5/824.short"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>paper<span class="nt" style="color: #000080;"></a></span> for more details). Currently metaSPAdes supports only a <span class="nt" style="color: #000080;"><strong><em></span>single<span class="nt" style="color: #000080;"></em></strong></span> short-read library which has to be <span class="nt" style="color: #000080;"><strong><em></span>paired-end<span class="nt" style="color: #000080;"></em></strong></span> (we hope to remove this restriction soon). In addition, you can provide long reads (e.g. using <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--pacbio<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--nanopore<span class="nt" style="color: #000080;"></code></span> options), but hybrid assembly for metagenomes remains an experimental pipeline and optimal performance is not guaranteed. It does not support <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#correctoropt"</span><span class="nt" style="color: #000080;">></span>careful mode<span class="nt" style="color: #000080;"></a></span> (mismatch correction is not available). In addition, you cannot specify coverage cutoff for metaSPAdes. Note that metaSPAdes might be very sensitive to presence of the technical sequences remaining in the data (most notably adapter readthroughs), please run quality control and pre-process your data accordingly.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC301" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC302" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"plasmid"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC303" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>--plasmid <span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code></span>plasmidspades.py<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC303" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--plasmid <span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>plasmidspades.py<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC304" class="line" lang="html">This flag is required when assembling only plasmids from WGS data sets (runs plasmidSPAdes, see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://academic.oup.com/bioinformatics/article/32/22/3380/2525610"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>paper<span class="nt" style="color: #000080;"></a></span> for the algorithm details). Note, that plasmidSPAdes is not compatible with <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sc"</span><span class="nt" style="color: #000080;">></span>single-cell mode<span class="nt" style="color: #000080;"></a></span>. Additionally, we do not recommend to run plasmidSPAdes on more than one library.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC305" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For plasmidSPAdes output details see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#plasmidout"</span><span class="nt" style="color: #000080;">></span>section 3.6<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC306" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC307" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"metaextrachromosomal"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC308" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>--metaplasmid <span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code></span>metaplasmidspades.py<span class="nt" style="color: #000080;"></code></span> and <span class="nt" style="color: #000080;"><code<span class="idiff left deletion" style="background-color: #fac5cd;">></span></span><span class="idiff deletion" style="background-color: #fac5cd;">--meta</span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;"></code></span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nt" style="color: #000080;"><span class="idiff right deletion" style="background-color: #fac5cd;"><code</span>></span>--plasmid<span class="nt" style="color: #000080;"></code></span>) and<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC309" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--metaviral <span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code></span>metaviralspades.py<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC308" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--metaplasmid <span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>metaplasmidspades.py<span class="nt" style="color: #000080;"></code></span> and <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">></span></span><span class="idiff addition" style="background-color: #c7f0d2;">--meta</span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;"></code></span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;"><code</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--plasmid<span class="nt" style="color: #000080;"></code></span>) and<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC309" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--metaviral <span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>metaviralspades.py<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC310" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>These options works specially for extracting extrachromosomal elements from metagenomic assemblies. They run similar pipelines that slightly differ in the simplification step; another difference is that for metaviral mode we output linear putative extrachromosomal contigs and for metaplasmid mode we do not.<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC311" class="line" lang="html">See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.cshlp.org/content/29/6/961.short"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>metaplasmid paper<span class="nt" style="color: #000080;"></a></span> and <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://academic.oup.com/bioinformatics/article-abstract/36/14/4126/5837667"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>metaviral paper<span class="nt" style="color: #000080;"></a></span> for the algorithms details.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC312" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For metaplasmidSPAdes/metaviralSPAdes output details see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#metapv"</span><span class="nt" style="color: #000080;">></span>section 3.7<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -314,138 +314,138 @@ See <a href="https://genome.cshlp.org/content/29/6/961.short" rel="nofollow">met</td>

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<td class="new_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC314" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Additionally for plasmidSPAdes, metaplasmidSPAdes and metaviralSPAdes we recommend to additionally verify resulting contigs with <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/ablab/viralVerify"</span><span class="nt" style="color: #000080;">></span>viralVerify tool<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC315" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC316" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"biosynthetic"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="new_line diff-line-num old" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC317" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>--bio <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC317" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--bio <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

318

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<td class="new_line diff-line-num" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC318" class="line" lang="html">This flag is required when assembling only non-ribosomal and polyketide gene clusters from WGS data sets (runs biosyntheticSPAdes, see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.cshlp.org/content/early/2019/06/03/gr.243477.118?top=1"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>paper<span class="nt" style="color: #000080;"></a></span> for the algorithm details). biosyntheticSPAdes is supposed to work on isolate or metagenomic WGS dataset. Note, that biosyntheticSPAdes is not compatible with any other modes. See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#bgc"</span><span class="nt" style="color: #000080;">></span>section 3.8<span class="nt" style="color: #000080;"></a></span> for biosyntheticSPAdes output details.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC319" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC320" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"rna"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

321

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<td class="new_line diff-line-num old" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC321" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>--rna <span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code></span>rnaspades.py<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

321

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC321" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--rna <span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>rnaspades.py<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

322

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<td class="new_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC322" class="line" lang="html">This flag should be used when assembling RNA-Seq data sets (runs rnaSPAdes). To learn more, see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"rnaspades_manual.html"</span><span class="nt" style="color: #000080;">></span>rnaSPAdes manual<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC323" class="line" lang="html">Not compatible with <span class="nt" style="color: #000080;"><code></span>--only-error-correction<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code></span>--careful<span class="nt" style="color: #000080;"></code></span> options.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC323" class="line" lang="html">Not compatible with <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--only-error-correction<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--careful<span class="nt" style="color: #000080;"></code></span> options.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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324

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<td class="new_line diff-line-num" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC324" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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325

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<td class="new_line diff-line-num" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC325" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"rnaviral"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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326

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<td class="new_line diff-line-num old" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC326" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>--rnaviral<span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code></span>rnaviralspades.py<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

326

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC326" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--rnaviral<span class="nt" style="color: #000080;"></code></span>   (same as <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>rnaviralspades.py<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

327

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<td class="new_line diff-line-num" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC327" class="line" lang="html">This flag should be used when assembling viral RNA-Seq data sets (runs rnaviralSPAdes).<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

328

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<td class="new_line diff-line-num old" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC328" class="line" lang="html">Not compatible with <span class="nt" style="color: #000080;"><code></span>--only-error-correction<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code></span>--careful<span class="nt" style="color: #000080;"></code></span> options.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

329

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<td class="new_line diff-line-num old" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC329" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--iontorrent <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

328

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC328" class="line" lang="html">Not compatible with <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--only-error-correction<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--careful<span class="nt" style="color: #000080;"></code></span> options.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

329

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC329" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--iontorrent <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

330

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<td class="new_line diff-line-num" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC330" class="line" lang="html">This flag is required when assembling IonTorrent data. Allows BAM files as input. Carefully read <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec3.3"</span><span class="nt" style="color: #000080;">></span>section 3.3<span class="nt" style="color: #000080;"></a></span> before using this option.<span class="nt" style="color: #000080;"></p></span></span>

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331

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<td class="new_line diff-line-num old" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC331" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--test<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="new_line diff-line-num new" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

331

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC331" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--test<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

332

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<td class="new_line diff-line-num" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC332" class="line" lang="html">Runs SPAdes on the toy data set; see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec2.4"</span><span class="nt" style="color: #000080;">></span>section 2.4<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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333

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC333" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code<span class="idiff left deletion" style="background-color: #fac5cd;">></span></span><span class="idiff deletion" style="background-color: #fac5cd;">-h</span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;"></code></span></span><span class="idiff deletion" style="background-color: #fac5cd;"> (or </span><span class="nt" style="color: #000080;"><span class="idiff right deletion" style="background-color: #fac5cd;"><code</span>></span>--help<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC333" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">></span></span><span class="idiff addition" style="background-color: #c7f0d2;">-h</span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;"></code></span></span><span class="idiff addition" style="background-color: #c7f0d2;"> (or </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;"><code</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--help<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC334" class="line" lang="html">Prints help.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC335" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code<span class="idiff left deletion" style="background-color: #fac5cd;">></span></span><span class="idiff deletion" style="background-color: #fac5cd;">-v</span><span class="nt" style="color: #000080;"><span class="idiff deletion" style="background-color: #fac5cd;"></code></span></span><span class="idiff deletion" style="background-color: #fac5cd;"> (or </span><span class="nt" style="color: #000080;"><span class="idiff right deletion" style="background-color: #fac5cd;"><code</span>></span>--version<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC335" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">></span></span><span class="idiff addition" style="background-color: #c7f0d2;">-v</span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;"></code></span></span><span class="idiff addition" style="background-color: #c7f0d2;"> (or </span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;"><code</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--version<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC336" class="line" lang="html">Prints SPAdes version.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC337" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC338" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"pipelineopt"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC339" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Pipeline options<span class="nt" style="color: #000080;"></h3></span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC340" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--only-error-correction<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC340" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--only-error-correction<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC341" class="line" lang="html">Performs read error correction only.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC342" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--only-assembler<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC342" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--only-assembler<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC343" class="line" lang="html">Runs assembly module only.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC344" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC345" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"correctoropt"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="new_line diff-line-num old" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC346" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>--careful<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC346" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--careful<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="new_line diff-line-num" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC347" class="line" lang="html">Tries to reduce the number of mismatches and short indels. Also runs MismatchCorrector - a post processing tool, which uses <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://bio-bwa.sourceforge.net"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>BWA<span class="nt" style="color: #000080;"></a></span> tool (comes with SPAdes). This option is recommended only for assembly of small genomes. We strongly recommend not to use it for large and medium-size eukaryotic genomes. Note, that this options is is not supported by metaSPAdes and rnaSPAdes.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC348" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--continue<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC348" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--continue<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="new_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC349" class="line" lang="html">Continues SPAdes run from the specified output folder starting from the last available check-point. Check-points are made after:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC350" class="line" lang="html"><span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC351" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>error correction module is finished<span class="nt" style="color: #000080;"></li></span></span>

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352

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<td class="new_line diff-line-num" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC352" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>iteration for each specified K value of assembly module is finished<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

353

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<td class="new_line diff-line-num" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC353" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>mismatch correction is finished for contigs or scaffolds<span class="nt" style="color: #000080;"></li></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC354" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>

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<td class="old_line diff-line-num old" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC355" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For example, if specified K values are 21, 33 and 55 and SPAdes was stopped or crashed during assembly stage with K = 55, you can run SPAdes with the <span class="nt" style="color: #000080;"><code></span>--continue<span class="nt" style="color: #000080;"></code></span> option specifying the same output directory. SPAdes will continue the run starting from the assembly stage with K = 55. Error correction module and iterations for K equal to 21 and 33 will not be run again. If <span class="nt" style="color: #000080;"><code></span>--continue<span class="nt" style="color: #000080;"></code></span> is set, the only allowed option is <span class="nt" style="color: #000080;"><code></span>-o <span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num old" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC356" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--restart-from <span class="ni" style="color: #800080;">&lt;</span>check_point<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC355" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For example, if specified K values are 21, 33 and 55 and SPAdes was stopped or crashed during assembly stage with K = 55, you can run SPAdes with the <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--continue<span class="nt" style="color: #000080;"></code></span> option specifying the same output directory. SPAdes will continue the run starting from the assembly stage with K = 55. Error correction module and iterations for K equal to 21 and 33 will not be run again. If <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--continue<span class="nt" style="color: #000080;"></code></span> is set, the only allowed option is <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-o <span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC356" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--restart-from <span class="ni" style="color: #800080;">&lt;</span>check_point<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="new_line diff-line-num" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC357" class="line" lang="html">Restart SPAdes run from the specified output folder starting from the specified check-point. Check-points are:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC358" class="line" lang="html"><span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="old_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC359" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>ec<span class="nt" style="color: #000080;"></code></span> - start from error correction<span class="nt" style="color: #000080;"></li></span></span>

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC360" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>as<span class="nt" style="color: #000080;"></code></span> - restart assembly module from the first iteration<span class="nt" style="color: #000080;"></li></span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC361" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>k<span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> - restart from the iteration with specified k values, e.g. k55 (not available in RNA-Seq mode)<span class="nt" style="color: #000080;"></li></span></span>

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362

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC362" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>mc<span class="nt" style="color: #000080;"></code></span> - restart mismatch correction<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC363" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>last<span class="nt" style="color: #000080;"></code></span> - restart from the last available check-point (similar to <span class="nt" style="color: #000080;"><code></span>--continue<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"></li></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC359" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>ec<span class="nt" style="color: #000080;"></code></span> - start from error correction<span class="nt" style="color: #000080;"></li></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC360" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>as<span class="nt" style="color: #000080;"></code></span> - restart assembly module from the first iteration<span class="nt" style="color: #000080;"></li></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC361" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>k<span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> - restart from the iteration with specified k values, e.g. k55 (not available in RNA-Seq mode)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC362" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>mc<span class="nt" style="color: #000080;"></code></span> - restart mismatch correction<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC363" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>last<span class="nt" style="color: #000080;"></code></span> - restart from the last available check-point (similar to <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--continue<span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"></li></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC364" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>

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<td class="new_line diff-line-num old" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC365" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In contrast to the <span class="nt" style="color: #000080;"><code></span>--continue<span class="nt" style="color: #000080;"></code></span> option, you can change some of the options when using <span class="nt" style="color: #000080;"><code></span>--restart-from<span class="nt" style="color: #000080;"></code></span>. You can change any option except: all basic options, all options for specifying input data (including <span class="nt" style="color: #000080;"><code></span>--dataset<span class="nt" style="color: #000080;"></code></span>), <span class="nt" style="color: #000080;"><code></span>--only-error-correction<span class="nt" style="color: #000080;"></code></span> option and <span class="nt" style="color: #000080;"><code></span>--only-assembler<span class="nt" style="color: #000080;"></code></span> option. For example, if you ran assembler with k values 21,33,55 without mismatch correction, you can add one more iteration with k=77 and run mismatch correction step by running SPAdes with following options:<span class="nt" style="color: #000080;"><br></span></span>

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<td class="new_line diff-line-num old" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC366" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>--restart-from k55 -k 21,33,55,77 --mismatch-correction -o <span class="ni" style="color: #800080;">&lt;</span>previous_output_dir<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC365" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In contrast to the <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--continue<span class="nt" style="color: #000080;"></code></span> option, you can change some of the options when using <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--restart-from<span class="nt" style="color: #000080;"></code></span>. You can change any option except: all basic options, all options for specifying input data (including <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--dataset<span class="nt" style="color: #000080;"></code></span>), <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--only-error-correction<span class="nt" style="color: #000080;"></code></span> option and <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--only-assembler<span class="nt" style="color: #000080;"></code></span> option. For example, if you ran assembler with k values 21,33,55 without mismatch correction, you can add one more iteration with k=77 and run mismatch correction step by running SPAdes with following options:<span class="nt" style="color: #000080;"><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC366" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--restart-from k55 -k 21,33,55,77 --mismatch-correction -o <span class="ni" style="color: #800080;">&lt;</span>previous_output_dir<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"><br></span></span>

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367

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<td class="new_line diff-line-num" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC367" class="line" lang="html">Since all files will be overwritten, do not forget to copy your assembly from the previous run if you need it.<span class="nt" style="color: #000080;"></p></span></span>

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368

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<td class="new_line diff-line-num old" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC368" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--disable-gzip-output<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

369

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<td class="new_line diff-line-num old" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC369" class="line" lang="html">Forces read error correction module not to compress the corrected reads. If this options is not set, corrected reads will be in <span class="nt" style="color: #000080;"><code></span>*.fastq.gz<span class="nt" style="color: #000080;"></code></span> format.<span class="nt" style="color: #000080;"></p></span></span>

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368

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC368" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--disable-gzip-output<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

369

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC369" class="line" lang="html">Forces read error correction module not to compress the corrected reads. If this options is not set, corrected reads will be in <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>*.fastq.gz<span class="nt" style="color: #000080;"></code></span> format.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC370" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC371" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"inputdata"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC372" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Input data<span class="nt" style="color: #000080;"></h3></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC373" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"inputdata:pairedend"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC374" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Specifying single library (paired-end or single-read)<span class="nt" style="color: #000080;"></h4></span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC375" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--12 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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375

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC375" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--12 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="new_line diff-line-num" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC376" class="line" lang="html">File with interlaced forward and reverse paired-end reads.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num old" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC377" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-1 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC377" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-1 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC378" class="line" lang="html">File with forward reads.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="new_line diff-line-num old" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC379" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-2 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC379" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-2 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC380" class="line" lang="html">File with reverse reads.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num old" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC381" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--merged <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC381" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--merged <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC382" class="line" lang="html">File with merged paired reads.<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

383

</td>

<td class="new_line diff-line-num" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

383

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC383" class="line" lang="html">If the properties of the library permit, overlapping paired-end reads can be merged using special software.<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

384

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<td class="new_line diff-line-num" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

384

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC384" class="line" lang="html">Non-empty files with (remaining) unmerged left/right reads (separate or interlaced) <span class="nt" style="color: #000080;"><strong></span>must<span class="nt" style="color: #000080;"></strong></span> be provided for the same library for SPAdes to correctly detect the original read length.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

385

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<td class="new_line diff-line-num old" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC385" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-s <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

385

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC385" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-s <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

386

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<td class="new_line diff-line-num" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

386

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC386" class="line" lang="html">File with unpaired reads.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

387

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<td class="new_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

387

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC387" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"inputdata:multiple"</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

388

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<td class="new_line diff-line-num" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

388

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC388" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Specifying multiple libraries<span class="nt" style="color: #000080;"></h4></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

389

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<td class="new_line diff-line-num" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

389

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC389" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><strong><em></span>Single-read libraries<span class="nt" style="color: #000080;"></em></strong></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

390

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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC390" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--s<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

391

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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC391" class="line" lang="html">File for single-read library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9). For example, for the first paired-end library the option is: <span class="nt" style="color: #000080;"><code></span>--s1 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

392

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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC392" class="line" lang="html">Do not use <span class="nt" style="color: #000080;"><code></span>-s<span class="nt" style="color: #000080;"></code></span> options for single-read libraries, since it specifies unpaired reads for the first paired-end library.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

390

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC390" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--s<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

391

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC391" class="line" lang="html">File for single-read library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9). For example, for the first paired-end library the option is: <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--s1 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

392

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC392" class="line" lang="html">Do not use <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-s<span class="nt" style="color: #000080;"></code></span> options for single-read libraries, since it specifies unpaired reads for the first paired-end library.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

393

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<td class="new_line diff-line-num" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC393" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><strong><em></span>Paired-end libraries<span class="nt" style="color: #000080;"></em></strong></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

394

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<td class="new_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC394" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-12 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

395

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<td class="new_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC395" class="line" lang="html">File with interlaced reads for paired-end library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9). For example, for the first single-read library the option is: <span class="nt" style="color: #000080;"><code></span>--pe1-12 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

396

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<td class="new_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC396" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-1 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

397

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<td class="new_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC397" class="line" lang="html">File with left reads for paired-end library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

398

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<td class="new_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC398" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-2 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

399

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<td class="new_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC399" class="line" lang="html">File with right reads for paired-end library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

400

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<td class="new_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC400" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-m <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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401

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<td class="new_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC401" class="line" lang="html">File with merged reads from paired-end library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

394

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC394" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-12 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

395

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC395" class="line" lang="html">File with interlaced reads for paired-end library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9). For example, for the first single-read library the option is: <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--pe1-12 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code></p></span></span>

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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

396

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC396" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-1 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

397

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC397" class="line" lang="html">File with left reads for paired-end library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

398

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC398" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-2 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

399

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC399" class="line" lang="html">File with right reads for paired-end library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC400" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-m <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC401" class="line" lang="html">File with merged reads from paired-end library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9)<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

402

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<td class="new_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC402" class="line" lang="html">If the properties of the library permit, paired reads can be merged using special software. Non-empty files with (remaining) unmerged left/right reads (separate or interlaced) <span class="nt" style="color: #000080;"><strong></span>must<span class="nt" style="color: #000080;"></strong></span> be provided for the same library for SPAdes to correctly detect the original read length.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

403

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<td class="new_line diff-line-num old" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC403" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-s <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

404

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<td class="new_line diff-line-num old" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC404" class="line" lang="html">File with unpaired reads from paired-end library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9)<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC403" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-s <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

404

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC404" class="line" lang="html">File with unpaired reads from paired-end library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9)<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

405

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<td class="new_line diff-line-num" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC405" class="line" lang="html">For example, paired reads can become unpaired during the error correction procedure.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

406

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<td class="new_line diff-line-num old" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC406" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-<span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

407

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<td class="new_line diff-line-num old" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC407" class="line" lang="html">Orientation of reads for paired-end library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9; <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = "fr","rf","ff").<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

408

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<td class="new_line diff-line-num old" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC408" class="line" lang="html">The default orientation for paired-end libraries is forward-reverse (<span class="nt" style="color: #000080;"><code></span>--<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>--<span class="nt" style="color: #000080;"></code></span>). For example, to specify reverse-forward orientation for the second paired-end library, you should use the flag: <span class="nt" style="color: #000080;"><code></span>--pe2-rf <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC406" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--pe<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-<span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

407

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC407" class="line" lang="html">Orientation of reads for paired-end library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9; <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = "fr","rf","ff").<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

408

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC408" class="line" lang="html">The default orientation for paired-end libraries is forward-reverse (<span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>--<span class="nt" style="color: #000080;"></code></span>). For example, to specify reverse-forward orientation for the second paired-end library, you should use the flag: <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--pe2-rf <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

409

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<td class="new_line diff-line-num" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

409

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC409" class="line" lang="html">Should not be confused with FR and RF strand-specificity for RNA-Seq data (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"rnaspades_manual.html#sec2.3"</span><span class="nt" style="color: #000080;">></span>rnaSPAdes manual<span class="nt" style="color: #000080;"></a></span>).<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

410

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<td class="new_line diff-line-num" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

410

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC410" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"inputdata:matepairs"</span><span class="nt" style="color: #000080;">></a><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

411

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<td class="new_line diff-line-num" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

411

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC411" class="line" lang="html"><span class="nt" style="color: #000080;"><strong><em></span>Mate-pair libraries<span class="nt" style="color: #000080;"></em></strong></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

412

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<td class="new_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC412" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--mp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-12 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

413

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<td class="new_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC413" class="line" lang="html">File with interlaced reads for mate-pair library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

414

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<td class="new_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC414" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--mp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-1 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

415

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<td class="new_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC415" class="line" lang="html">File with left reads for mate-pair library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

416

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<td class="new_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC416" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--mp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-2 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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417

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<td class="new_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC417" class="line" lang="html">File with right reads for mate-pair library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

418

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<td class="new_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC418" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--mp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-<span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

419

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<td class="new_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC419" class="line" lang="html">Orientation of reads for mate-pair library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9; <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = "fr","rf","ff").<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

420

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<td class="new_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC420" class="line" lang="html">The default orientation for mate-pair libraries is reverse-forward (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>-- --<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>). For example, to specify forward-forward orientation for the first mate-pair library, you should use the flag: <span class="nt" style="color: #000080;"><code></span>--mp1-ff <span class="nt" style="color: #000080;"></code></p></span></span>

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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC412" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--mp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-12 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

413

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC413" class="line" lang="html">File with interlaced reads for mate-pair library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

414

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC414" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--mp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-1 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

415

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC415" class="line" lang="html">File with left reads for mate-pair library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

416

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC416" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--mp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-2 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC417" class="line" lang="html">File with right reads for mate-pair library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

418

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC418" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--mp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-<span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

419

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC419" class="line" lang="html">Orientation of reads for mate-pair library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9; <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = "fr","rf","ff").<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

420

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC420" class="line" lang="html">The default orientation for mate-pair libraries is reverse-forward (<span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>-- --<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>). For example, to specify forward-forward orientation for the first mate-pair library, you should use the flag: <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--mp1-ff <span class="nt" style="color: #000080;"></code></p></span></span>

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421

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<td class="new_line diff-line-num" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

421

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC421" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hqmp"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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422

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<td class="new_line diff-line-num" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

422

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC422" class="line" lang="html"><span class="nt" style="color: #000080;"><strong><em></span>High-quality mate-pair libraries<span class="nt" style="color: #000080;"></em></strong></span> (can be used for mate-pair only assembly)<span class="nt" style="color: #000080;"></p></span></span>

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423

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC423" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--hqmp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-12 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

424

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC424" class="line" lang="html">File with interlaced reads for high-quality mate-pair library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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425

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC425" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--hqmp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-1 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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426

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC426" class="line" lang="html">File with left reads for high-quality mate-pair library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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427

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC427" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--hqmp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-2 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

428

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC428" class="line" lang="html">File with right reads for high-quality mate-pair library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

429

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC429" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--hqmp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-s <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

430

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC430" class="line" lang="html">File with unpaired reads from high-quality mate-pair library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9)<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

431

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC431" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--hqmp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-<span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

432

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC432" class="line" lang="html">Orientation of reads for high-quality mate-pair library number <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9; <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = "fr","rf","ff").<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

433

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC433" class="line" lang="html">The default orientation for high-quality mate-pair libraries is forward-reverse (<span class="nt" style="color: #000080;"><code></span>--<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>--<span class="nt" style="color: #000080;"></code></span>). For example, to specify reverse-forward orientation for the first high-quality mate-pair library, you should use the flag: <span class="nt" style="color: #000080;"><code></span>--hqmp1-rf <span class="nt" style="color: #000080;"></code></p></span></span>

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<td class="new_line diff-line-num new" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

423

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC423" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--hqmp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-12 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

424

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC424" class="line" lang="html">File with interlaced reads for high-quality mate-pair library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

425

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC425" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--hqmp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-1 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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426

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC426" class="line" lang="html">File with left reads for high-quality mate-pair library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

427

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC427" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--hqmp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-2 <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

428

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC428" class="line" lang="html">File with right reads for high-quality mate-pair library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

429

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC429" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--hqmp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-s <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

430

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC430" class="line" lang="html">File with unpaired reads from high-quality mate-pair library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9)<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num new" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

431

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC431" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--hqmp<span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span>-<span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

432

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC432" class="line" lang="html">Orientation of reads for high-quality mate-pair library number <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>#<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = 1,2,..,9; <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>or<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> = "fr","rf","ff").<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

433

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC433" class="line" lang="html">The default orientation for high-quality mate-pair libraries is forward-reverse (<span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>--<span class="nt" style="color: #000080;"></code></span>). For example, to specify reverse-forward orientation for the first high-quality mate-pair library, you should use the flag: <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--hqmp1-rf <span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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434

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<td class="new_line diff-line-num" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC434" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"inputdata:longreads"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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435

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC435" class="line" lang="html"><span class="nt" style="color: #000080;"><strong><em></span>Specifying data for hybrid assembly<span class="nt" style="color: #000080;"></em></strong></p></span></span>

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436

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC436" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--pacbio <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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437

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<td class="new_line diff-line-num old" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC437" class="line" lang="html">File with PacBio CLR reads. For PacBio CCS reads use <span class="nt" style="color: #000080;"><code></span>-s<span class="nt" style="color: #000080;"></code></span> option. More information on PacBio reads is provided in section 3.1.<span class="nt" style="color: #000080;"></p></span></span>

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438

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<td class="new_line diff-line-num old" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC438" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--nanopore <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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436

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC436" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--pacbio <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="new_line diff-line-num new" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

437

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC437" class="line" lang="html">File with PacBio CLR reads. For PacBio CCS reads use <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-s<span class="nt" style="color: #000080;"></code></span> option. More information on PacBio reads is provided in section 3.1.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC438" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--nanopore <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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439

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC439" class="line" lang="html">File with Oxford Nanopore reads.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC440" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--sanger <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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440

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC440" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--sanger <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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441

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC441" class="line" lang="html">File with Sanger reads<span class="nt" style="color: #000080;"></p></span></span>

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442

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC442" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--trusted-contigs <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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442

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC442" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--trusted-contigs <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

443

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<td class="new_line diff-line-num" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC443" class="line" lang="html">Reliable contigs of the same genome, which are likely to have no misassemblies and small rate of other errors (e.g. mismatches and indels). This option is not intended for contigs of the related species.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

444

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<td class="new_line diff-line-num old" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC444" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--untrusted-contigs <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

444

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC444" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--untrusted-contigs <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

445

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<td class="new_line diff-line-num" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

445

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC445" class="line" lang="html">Contigs of the same genome, quality of which is average or unknown. Contigs of poor quality can be used but may introduce errors in the assembly. This option is also not intended for contigs of the related species.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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446

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<td class="new_line diff-line-num" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

446

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC446" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><strong><em></span>Other input<span class="nt" style="color: #000080;"></em></strong></p></span></span>

</pre></td>

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447

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<td class="new_line diff-line-num old" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC447" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--assembly-graph <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

448

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<td class="new_line diff-line-num old" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC448" class="line" lang="html">File with assembly graph. Could only be used in plasmid, metaplasmid, metaviral and biosynthetic mode. The primary purpose of this option to run these pipelines on already constructed and simplified assembly graph this way skipping a large part of SPAdes pipeline. Original reads the graph was constructed from need to be specified as well. Exact k-mer length (via <span class="nt" style="color: #000080;"><code></span>-k<span class="nt" style="color: #000080;"></code></span> option) should be provided. Note that the output would be different as compared to standalone runs of these pipelines as they setup graph simplification options as well.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

447

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC447" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--assembly-graph <span class="ni" style="color: #800080;">&lt;</span>file_name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

448

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC448" class="line" lang="html">File with assembly graph. Could only be used in plasmid, metaplasmid, metaviral and biosynthetic mode. The primary purpose of this option to run these pipelines on already constructed and simplified assembly graph this way skipping a large part of SPAdes pipeline. Original reads the graph was constructed from need to be specified as well. Exact k-mer length (via <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-k<span class="nt" style="color: #000080;"></code></span> option) should be provided. Note that the output would be different as compared to standalone runs of these pipelines as they setup graph simplification options as well.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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449

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC449" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"inputdata:yaml"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC450" class="line" lang="html"><span class="nt" style="color: #000080;"><strong><em></span>Specifying input data with YAML data set file (advanced)<span class="nt" style="color: #000080;"></em></strong></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC451" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>An alternative way to specify an input data set for SPAdes is to create a <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://www.yaml.org/"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>YAML<span class="nt" style="color: #000080;"></a></span> data set file. By using a YAML file you can provide an unlimited number of paired-end, mate-pair and unpaired libraries. Basically, YAML data set file is a text file, in which input libraries are provided as a comma-separated list in square brackets. Each library is provided in braces as a comma-separated list of attributes. The following attributes are available:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -508,33 +508,33 @@ File with assembly graph. Could only be used in plasmid, metaplasmid, metaviral</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC508" class="line" lang="html">        ]</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC509" class="line" lang="html">      }</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC510" class="line" lang="html">    ]<span class="nt" style="color: #000080;"></pre></div></span></span>

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<td class="old_line diff-line-num old" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

511

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<td class="new_line diff-line-num old" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC511" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Once you have created a YAML file save it with <span class="nt" style="color: #000080;"><code></span>.yaml<span class="nt" style="color: #000080;"></code></span> extension (e.g. as <span class="nt" style="color: #000080;"><code></span>my_data_set.yaml<span class="nt" style="color: #000080;"></code></span>) and run SPAdes using the <span class="nt" style="color: #000080;"><code></span>--dataset<span class="nt" style="color: #000080;"></code></span> option:<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

512

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<td class="new_line diff-line-num old" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC512" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>--dataset <span class="ni" style="color: #800080;">&lt;</span>your YAML file<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="new_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

511

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC511" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Once you have created a YAML file save it with <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>.yaml<span class="nt" style="color: #000080;"></code></span> extension (e.g. as <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>my_data_set.yaml<span class="nt" style="color: #000080;"></code></span>) and run SPAdes using the <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--dataset<span class="nt" style="color: #000080;"></code></span> option:<span class="nt" style="color: #000080;"><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC512" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--dataset <span class="ni" style="color: #800080;">&lt;</span>your YAML file<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="new_line diff-line-num" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC513" class="line" lang="html">Notes:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC514" class="line" lang="html"><span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="old_line diff-line-num old" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC515" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>The <span class="nt" style="color: #000080;"><code></span>--dataset<span class="nt" style="color: #000080;"></code></span> option cannot be used with any other options for specifying input data.<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num new" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC515" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>The <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--dataset<span class="nt" style="color: #000080;"></code></span> option cannot be used with any other options for specifying input data.<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC516" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>We recommend to nest all files with long reads of the same data type in a single library block.<span class="nt" style="color: #000080;"></li></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC517" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC518" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC519" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"advancedopt"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

520

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<td class="new_line diff-line-num" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC520" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Advanced options<span class="nt" style="color: #000080;"></h3></span></span>

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<td class="old_line diff-line-num old" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

521

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<td class="new_line diff-line-num old" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC521" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-t <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (or <span class="nt" style="color: #000080;"><code></span>--threads <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC521" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-t <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (or <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--threads <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

522

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<td class="new_line diff-line-num" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC522" class="line" lang="html">Number of threads. The default value is 16.<span class="nt" style="color: #000080;"></p></span></span>

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523

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<td class="new_line diff-line-num old" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC523" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-m <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (or <span class="nt" style="color: #000080;"><code></span>--memory <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC523" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-m <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> (or <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--memory <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>)<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC524" class="line" lang="html">Set memory limit in Gb. SPAdes terminates if it reaches this limit. The default value is 250 Gb. Actual amount of consumed RAM will be below this limit. Make sure this value is correct for the given machine. SPAdes uses the limit value to automatically determine the sizes of various buffers, etc.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num old" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC525" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--tmp-dir <span class="ni" style="color: #800080;">&lt;</span>dir_name<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="new_line diff-line-num old" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC526" class="line" lang="html">Set directory for temporary files from read error correction. The default value is <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/corrected/tmp<span class="nt" style="color: #000080;"></code></p></span></span>

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<td class="new_line diff-line-num old" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC527" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-k <span class="ni" style="color: #800080;">&lt;</span>int,int,...<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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528

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<td class="new_line diff-line-num old" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC528" class="line" lang="html">Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128 and listed in ascending order). If <span class="nt" style="color: #000080;"><code></span>--sc<span class="nt" style="color: #000080;"></code></span> is set the default values are 21,33,55. For multicell data sets K values are automatically selected using maximum read length (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec3.4"</span><span class="nt" style="color: #000080;">></span>see note for assembling long Illumina paired reads for details<span class="nt" style="color: #000080;"></a></span>). To properly select K values for IonTorrent data read <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec3.3"</span><span class="nt" style="color: #000080;">></span>section 3.3<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC529" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--cov-cutoff <span class="ni" style="color: #800080;">&lt;</span>float<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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525

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC525" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--tmp-dir <span class="ni" style="color: #800080;">&lt;</span>dir_name<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="new_line diff-line-num new" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC526" class="line" lang="html">Set directory for temporary files from read error correction. The default value is <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/corrected/tmp<span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC527" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-k <span class="ni" style="color: #800080;">&lt;</span>int,int,...<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC528" class="line" lang="html">Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128 and listed in ascending order). If <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--sc<span class="nt" style="color: #000080;"></code></span> is set the default values are 21,33,55. For multicell data sets K values are automatically selected using maximum read length (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec3.4"</span><span class="nt" style="color: #000080;">></span>see note for assembling long Illumina paired reads for details<span class="nt" style="color: #000080;"></a></span>). To properly select K values for IonTorrent data read <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec3.3"</span><span class="nt" style="color: #000080;">></span>section 3.3<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC529" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--cov-cutoff <span class="ni" style="color: #800080;">&lt;</span>float<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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530

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<td class="new_line diff-line-num" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

530

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC530" class="line" lang="html">Read coverage cutoff value. Must be a positive float value, or "auto", or "off". Default value is "off". When set to "auto" SPAdes automatically computes coverage threshold using conservative strategy. Note, that this option is not supported by metaSPAdes.<span class="nt" style="color: #000080;"></p></span></span>

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531

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<td class="new_line diff-line-num old" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC531" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--phred-offset <span class="ni" style="color: #800080;">&lt;</span>33 or 64<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC531" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--phred-offset <span class="ni" style="color: #800080;">&lt;</span>33 or 64<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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532

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<td class="new_line diff-line-num" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

532

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC532" class="line" lang="html">PHRED quality offset for the input reads, can be either 33 or 64. It will be auto-detected if it is not specified.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC533" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>--custom-hmms <span class="ni" style="color: #800080;">&lt;</span>file or directory<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC533" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--custom-hmms <span class="ni" style="color: #800080;">&lt;</span>file or directory<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC534" class="line" lang="html">File or directory with amino acid HMMs for <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#hmm"</span><span class="nt" style="color: #000080;">></span>HMM-guided mode<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC535" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"examples"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC536" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Examples<span class="nt" style="color: #000080;"></h3></span></span>

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537

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<td class="new_line diff-line-num old" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC537" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To test the toy data set, you can also run the following command from the SPAdes <span class="nt" style="color: #000080;"><code></span>bin<span class="nt" style="color: #000080;"></code></span> directory:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num new" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC537" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To test the toy data set, you can also run the following command from the SPAdes <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>bin<span class="nt" style="color: #000080;"></code></span> directory:<span class="nt" style="color: #000080;"></p></span></span>

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538

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<td class="new_line diff-line-num" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC538" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    spades.py --pe1-1 ../share/spades/test_dataset/ecoli_1K_1.fq.gz \</span>

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<td class="old_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC539" class="line" lang="html">    --pe1-2 ../share/spades/test_dataset/ecoli_1K_2.fq.gz -o spades_test<span class="nt" style="color: #000080;"></pre></div></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC540" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>If you have your library separated into several pairs of files, for example:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -585,9 +585,9 @@ File or directory with amino acid HMMs for <a href="#hmm">HMM-guided mode</a>.</</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC585" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec3.3"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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586

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<td class="new_line diff-line-num" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC586" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Assembling IonTorrent reads<span class="nt" style="color: #000080;"></h2></span></span>

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<td class="old_line diff-line-num" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

587

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<td class="new_line diff-line-num" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC587" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Only FASTQ or BAM files are supported as input.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

588

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<td class="new_line diff-line-num old" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC588" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec3.4"</span><span class="nt" style="color: #000080;">></span>recommendation for long reads<span class="nt" style="color: #000080;"></a></span> (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: <span class="nt" style="color: #000080;"><code></span>--restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <span class="ni" style="color: #800080;">&lt;</span>previous_output_dir<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>. Do not forget to copy contigs and scaffolds from the previous run. We are planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC588" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec3.4"</span><span class="nt" style="color: #000080;">></span>recommendation for long reads<span class="nt" style="color: #000080;"></a></span> (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <span class="ni" style="color: #800080;">&lt;</span>previous_output_dir<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>. Do not forget to copy contigs and scaffolds from the previous run. We are planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC589" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>You may need no error correction for Hi-Q enzyme at all. However, we suggest trying to assemble your data with and without error correction and select the best variant.<span class="nt" style="color: #000080;"></p></span></span>

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590

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<td class="new_line diff-line-num old" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC590" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For non-trivial datasets (e.g. with high GC, low or uneven coverage) we suggest to enable single-cell mode (setting <span class="nt" style="color: #000080;"><code></span>--sc<span class="nt" style="color: #000080;"></code></span> option) and use k-mer lengths of 21,33,55. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="new_line diff-line-num new" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

590

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC590" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For non-trivial datasets (e.g. with high GC, low or uneven coverage) we suggest to enable single-cell mode (setting <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--sc<span class="nt" style="color: #000080;"></code></span> option) and use k-mer lengths of 21,33,55. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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591

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC591" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec3.4"</span><span class="nt" style="color: #000080;">></a><br></span></span>

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592

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<td class="new_line diff-line-num" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

592

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC592" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"illumina_long"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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593

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<td class="new_line diff-line-num" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC593" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Assembling long Illumina paired reads (2x150 and 2x250)<span class="nt" style="color: #000080;"></h2></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -598,7 +598,7 @@ File or directory with amino acid HMMs for <a href="#hmm">HMM-guided mode</a>.</</td>

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<td class="new_line diff-line-num" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC598" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Multi-cell data set with read length 2x150 bp<span class="nt" style="color: #000080;"></h3></span></span>

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599

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<td class="new_line diff-line-num" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC599" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Do not turn off SPAdes error correction (BayesHammer module), which is included in SPAdes default pipeline.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC600" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>If you have enough coverage (50x+), then you may want to try to set k-mer lengths of 21, 33, 55, 77 (selected by default for reads with length 150bp).<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

601

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<td class="new_line diff-line-num old" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC601" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Make sure you run assembler with the <span class="nt" style="color: #000080;"><code></span>--careful<span class="nt" style="color: #000080;"></code></span> option to minimize number of mismatches in the final contigs.<span class="nt" style="color: #000080;"></p></span></span>

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601

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC601" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Make sure you run assembler with the <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--careful<span class="nt" style="color: #000080;"></code></span> option to minimize number of mismatches in the final contigs.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC602" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>We recommend that you check the SPAdes log file at the end of the each iteration to control the average coverage of the contigs.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

603

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<td class="new_line diff-line-num" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

603

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC603" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For reads corrected prior to running the assembler:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

604

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<td class="new_line diff-line-num" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

604

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC604" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    spades.py -k 21,33,55,77 --careful --only-assembler <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-k"</span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span><span class="nt" style="color: #000080;"></span></span>your reads<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-k"</span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></span></span> -o spades_output<span class="nt" style="color: #000080;"></pre></div></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -608,7 +608,7 @@ File or directory with amino acid HMMs for <a href="#hmm">HMM-guided mode</a>.</</td>

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<td class="old_line diff-line-num" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

608

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<td class="new_line diff-line-num" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

608

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC608" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Multi-cell data set with read lengths 2x250 bp<span class="nt" style="color: #000080;"></h3></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

609

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<td class="new_line diff-line-num" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

609

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC609" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Do not turn off SPAdes error correction (BayesHammer module), which is included in SPAdes default pipeline.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

610

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<td class="new_line diff-line-num" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

610

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC610" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>By default we suggest to increase k-mer lengths in increments of 22 until the k-mer length reaches 127. The exact length of the k-mer depends on the coverage: k-mer length of 127 corresponds to 50x k-mer coverage and higher. For read length 250bp SPAdes automatically chooses K values equal to 21, 33, 55, 77, 99, 127.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

611

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<td class="new_line diff-line-num old" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC611" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Make sure you run assembler with <span class="nt" style="color: #000080;"><code></span>--careful<span class="nt" style="color: #000080;"></code></span> option to minimize number of mismatches in the final contigs.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

611

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC611" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Make sure you run assembler with <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--careful<span class="nt" style="color: #000080;"></code></span> option to minimize number of mismatches in the final contigs.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

612

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<td class="new_line diff-line-num" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC612" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>We recommend you to check the SPAdes log file at the end of the each iteration to control the average coverage of the contigs.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

613

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<td class="new_line diff-line-num" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

613

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC613" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For reads corrected prior to running the assembler:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

614

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<td class="new_line diff-line-num" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

614

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC614" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight highlight-source-shell"</span><span class="nt" style="color: #000080;">><pre></span>    spades.py -k 21,33,55,77,99,127 --careful --only-assembler <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-k"</span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span><span class="nt" style="color: #000080;"></span></span>your reads<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pl-k"</span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></span></span> -o spades_output<span class="nt" style="color: #000080;"></pre></div></span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -622,50 +622,50 @@ File or directory with amino acid HMMs for <a href="#hmm">HMM-guided mode</a>.</</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC622" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hmm"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC623" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>HMM-guided mode<span class="nt" style="color: #000080;"></h2></span></span>

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<td class="old_line diff-line-num" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC624" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The majority of SPAdes assembly modes (normal multicell, single-cell, rnaviral, meta and of course biosynthetic) also supports HMM-guided mode as implemented in biosyntheticSPAdes. The detailed description could be found in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.cshlp.org/content/early/2019/06/03/gr.243477.118"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>biosyntheticSPAdes paper<span class="nt" style="color: #000080;"></a></span>, but in short: amino acid profile HMMs are aligned to the edges of assembly graph. After this the subgraphs containing the set of matches ("domains") are extracted and all possible paths through the domains that are supported both by paired-end data (via scaffolds) and graph topology are obtained (putative biosynthetic gene clusters).<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC625" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>HMM-guided mode could be enabled via providing a set of HMMs via <span class="nt" style="color: #000080;"><code></span>--custom-hmms<span class="nt" style="color: #000080;"></code></span> option. In HMM guided mode the set of contigs and scaffolds (see section <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#spadesoutput"</span><span class="nt" style="color: #000080;">></span>SPAdes output<span class="nt" style="color: #000080;"></a></span> for more information about SPAdes output) is kept intact, however additional <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#bgc"</span><span class="nt" style="color: #000080;">></span>biosyntheticSPAdes output<span class="nt" style="color: #000080;"></a></span> represents the output of HMM-guided assembly.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num old" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC626" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Note that normal biosyntheticSPAdes mode (via <span class="nt" style="color: #000080;"><code></span>--bio<span class="nt" style="color: #000080;"></code></span> option) is a bit different from HMM-guided mode: besides using the special set of profile HMMS representing a family of NRSP/PKS domains also includes a set of assembly graph simplification and processing settings aimed for fuller recovery of biosynthetic gene clusters.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC627" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Given an increased interest in coronavirus research we developed a coronavirus assembly mode for SPAdes assembler (also known as coronaSPAdes). It allows to assemble full-length coronaviridae genomes from the transcriptomic and metatranscriptomic data. Algorithmically, coronaSPAdes is an rnaviralSPAdes that uses the set of HMMs from Pfam SARS-CoV-2 2.0 set as well as additional HMMs as outlined by <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://doi.org/10.1093/ve/vey035"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>(Phan et al, 2019)<span class="nt" style="color: #000080;"></a></span>. coronaSPAdes could be run via a dedicated <span class="nt" style="color: #000080;"><code></span>coronaspades.py<span class="nt" style="color: #000080;"></code></span> script. See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://www.biorxiv.org/content/10.1101/2020.07.28.224584v1"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>coronaSPAdes preprint<span class="nt" style="color: #000080;"></a></span> for more information about rnaviralSPAdes,  coronaSPAdes and HMM-guided mode. Output for any HMM-related mode (--bio, --corona, or --custom-hmms flags) is the same with biosyntheticSPAdes' output.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC625" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>HMM-guided mode could be enabled via providing a set of HMMs via <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--custom-hmms<span class="nt" style="color: #000080;"></code></span> option. In HMM guided mode the set of contigs and scaffolds (see section <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#spadesoutput"</span><span class="nt" style="color: #000080;">></span>SPAdes output<span class="nt" style="color: #000080;"></a></span> for more information about SPAdes output) is kept intact, however additional <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#bgc"</span><span class="nt" style="color: #000080;">></span>biosyntheticSPAdes output<span class="nt" style="color: #000080;"></a></span> represents the output of HMM-guided assembly.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num new" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC626" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Note that normal biosyntheticSPAdes mode (via <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>--bio<span class="nt" style="color: #000080;"></code></span> option) is a bit different from HMM-guided mode: besides using the special set of profile HMMS representing a family of NRSP/PKS domains also includes a set of assembly graph simplification and processing settings aimed for fuller recovery of biosynthetic gene clusters.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC627" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Given an increased interest in coronavirus research we developed a coronavirus assembly mode for SPAdes assembler (also known as coronaSPAdes). It allows to assemble full-length coronaviridae genomes from the transcriptomic and metatranscriptomic data. Algorithmically, coronaSPAdes is an rnaviralSPAdes that uses the set of HMMs from Pfam SARS-CoV-2 2.0 set as well as additional HMMs as outlined by <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://doi.org/10.1093/ve/vey035"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>(Phan et al, 2019)<span class="nt" style="color: #000080;"></a></span>. coronaSPAdes could be run via a dedicated <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>coronaspades.py<span class="nt" style="color: #000080;"></code></span> script. See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://www.biorxiv.org/content/10.1101/2020.07.28.224584v1"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>coronaSPAdes preprint<span class="nt" style="color: #000080;"></a></span> for more information about rnaviralSPAdes,  coronaSPAdes and HMM-guided mode. Output for any HMM-related mode (--bio, --corona, or --custom-hmms flags) is the same with biosyntheticSPAdes' output.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC628" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"spadesoutput"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC629" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes output<span class="nt" style="color: #000080;"></h2></span></span>

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<td class="old_line diff-line-num old" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC630" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes stores all output files in <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code></span>, which is set by the user.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC630" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes stores all output files in <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code></span>, which is set by the user.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC631" class="line" lang="html"><span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="new_line diff-line-num old" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC632" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/corrected/<span class="nt" style="color: #000080;"></code></span> directory contains reads corrected by BayesHammer in <span class="nt" style="color: #000080;"><code></span>*.fastq.gz<span class="nt" style="color: #000080;"></code></span> files; if compression is disabled, reads are stored in uncompressed <span class="nt" style="color: #000080;"><code></span>*.fastq<span class="nt" style="color: #000080;"></code></span> files<span class="nt" style="color: #000080;"></li></span></span>

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<td class="new_line diff-line-num old" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC633" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/scaffolds.fasta<span class="nt" style="color: #000080;"></code></span> contains resulting scaffolds (recommended for use as resulting sequences)<span class="nt" style="color: #000080;"></li></span></span>

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<td class="new_line diff-line-num old" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC634" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/contigs.fasta<span class="nt" style="color: #000080;"></code></span> contains resulting contigs<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num old" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC635" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/assembly_graph_with_scaffolds.gfa<span class="nt" style="color: #000080;"></code></span> contains SPAdes assembly graph and scaffolds paths in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md"</span><span class="nt" style="color: #000080;">></span>GFA 1.0 format<span class="nt" style="color: #000080;"></a></li></span></span>

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636

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<td class="new_line diff-line-num old" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC636" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/assembly_graph.fastg<span class="nt" style="color: #000080;"></code></span> contains SPAdes assembly graph in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>FASTG format<span class="nt" style="color: #000080;"></a></li></span></span>

</pre></td>

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637

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<td class="new_line diff-line-num old" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC637" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/contigs.paths<span class="nt" style="color: #000080;"></code></span> contains paths in the assembly graph corresponding to contigs.fasta (see details below)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

638

</td>

<td class="new_line diff-line-num old" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC638" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/scaffolds.paths<span class="nt" style="color: #000080;"></code></span> contains paths in the assembly graph corresponding to scaffolds.fasta (see details below)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

632

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC632" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/corrected/<span class="nt" style="color: #000080;"></code></span> directory contains reads corrected by BayesHammer in <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>*.fastq.gz<span class="nt" style="color: #000080;"></code></span> files; if compression is disabled, reads are stored in uncompressed <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>*.fastq<span class="nt" style="color: #000080;"></code></span> files<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

633

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC633" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/scaffolds.fasta<span class="nt" style="color: #000080;"></code></span> contains resulting scaffolds (recommended for use as resulting sequences)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

634

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC634" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/contigs.fasta<span class="nt" style="color: #000080;"></code></span> contains resulting contigs<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

635

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC635" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/assembly_graph_with_scaffolds.gfa<span class="nt" style="color: #000080;"></code></span> contains SPAdes assembly graph and scaffolds paths in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md"</span><span class="nt" style="color: #000080;">></span>GFA 1.0 format<span class="nt" style="color: #000080;"></a></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

636

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC636" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/assembly_graph.fastg<span class="nt" style="color: #000080;"></code></span> contains SPAdes assembly graph in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>FASTG format<span class="nt" style="color: #000080;"></a></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

637

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC637" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/contigs.paths<span class="nt" style="color: #000080;"></code></span> contains paths in the assembly graph corresponding to contigs.fasta (see details below)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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638

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC638" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/scaffolds.paths<span class="nt" style="color: #000080;"></code></span> contains paths in the assembly graph corresponding to scaffolds.fasta (see details below)<span class="nt" style="color: #000080;"></li></span></span>

</pre></td>

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639

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639

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC639" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>

</pre></td>

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640

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<td class="new_line diff-line-num" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

640

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC640" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"spadesoutput:contigs"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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641

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641

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC641" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Contigs and scaffolds format<span class="nt" style="color: #000080;"></h3></span></span>

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642

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<td class="new_line diff-line-num" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

642

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC642" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Contigs/scaffolds names in SPAdes output FASTA files have the following format:<span class="nt" style="color: #000080;"><br></span></span>

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643

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<td class="new_line diff-line-num old" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC643" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&gt;</span>NODE_3_length_237403_cov_243.207<span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

644

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<td class="new_line diff-line-num old" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC644" class="line" lang="html">Here <span class="nt" style="color: #000080;"><code></span>3<span class="nt" style="color: #000080;"></code></span> is the number of the contig/scaffold, <span class="nt" style="color: #000080;"><code></span>237403<span class="nt" style="color: #000080;"></code></span> is the sequence length in nucleotides and <span class="nt" style="color: #000080;"><code></span>243.207<span class="nt" style="color: #000080;"></code></span> is the k-mer coverage for the last (largest) k value used. Note that the k-mer coverage is always lower than the read (per-base) coverage.<span class="nt" style="color: #000080;"></p></span></span>

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643

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC643" class="line" lang="html"><span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&gt;</span>NODE_3_length_237403_cov_243.207<span class="nt" style="color: #000080;"></code><br></span></span>

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644

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC644" class="line" lang="html">Here <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>3<span class="nt" style="color: #000080;"></code></span> is the number of the contig/scaffold, <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>237403<span class="nt" style="color: #000080;"></code></span> is the sequence length in nucleotides and <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>243.207<span class="nt" style="color: #000080;"></code></span> is the k-mer coverage for the last (largest) k value used. Note that the k-mer coverage is always lower than the read (per-base) coverage.<span class="nt" style="color: #000080;"></p></span></span>

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645

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<td class="new_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

645

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC645" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In general, SPAdes uses two techniques for joining contigs into scaffolds. First one relies on read pairs and tries to estimate the size of the gap separating contigs. The second one relies on the assembly graph: e.g. if two contigs are separated by a complex tandem repeat, that cannot be resolved exactly, contigs are joined into scaffold with a fixed gap size of 100 bp. Contigs produced by SPAdes do not contain N symbols.<span class="nt" style="color: #000080;"></p></span></span>

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646

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC646" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"spadesoutput:graph"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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647

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647

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC647" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Assembly graph formats<span class="nt" style="color: #000080;"></h3></span></span>

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648

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<td class="new_line diff-line-num old" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC648" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To view FASTG and GFA files we recommend to use <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://rrwick.github.io/Bandage/"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>Bandage visualization tool<span class="nt" style="color: #000080;"></a></span>. Note that sequences stored in <span class="nt" style="color: #000080;"><code></span>assembly_graph.fastg<span class="nt" style="color: #000080;"></code></span> correspond to contigs before repeat resolution (edges of the assembly graph). Paths corresponding to contigs after repeat resolution (scaffolding) are stored in <span class="nt" style="color: #000080;"><code></span>contigs.paths<span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code></span>scaffolds.paths<span class="nt" style="color: #000080;"></code></span>) in the format accepted by Bandage (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/rrwick/Bandage/wiki/Graph-paths"</span><span class="nt" style="color: #000080;">></span>Bandage wiki<span class="nt" style="color: #000080;"></a></span> for details). The example is given below.<span class="nt" style="color: #000080;"></p></span></span>

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649

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<td class="new_line diff-line-num old" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC649" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Let the contig with the name <span class="nt" style="color: #000080;"><code></span>NODE_5_length_100000_cov_215.651<span class="nt" style="color: #000080;"></code></span> consist of the following edges of the assembly graph:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

650

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<td class="new_line diff-line-num old" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC650" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;"><span class="idiff left right deletion" style="background-color: #fac5cd;">><code</span>></span>    <span class="ni" style="color: #800080;">&gt;</span>EDGE_2_length_33280_cov_199.702</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

648

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC648" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To view FASTG and GFA files we recommend to use <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://rrwick.github.io/Bandage/"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>Bandage visualization tool<span class="nt" style="color: #000080;"></a></span>. Note that sequences stored in <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>assembly_graph.fastg<span class="nt" style="color: #000080;"></code></span> correspond to contigs before repeat resolution (edges of the assembly graph). Paths corresponding to contigs after repeat resolution (scaffolding) are stored in <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>contigs.paths<span class="nt" style="color: #000080;"></code></span> (<span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>scaffolds.paths<span class="nt" style="color: #000080;"></code></span>) in the format accepted by Bandage (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/rrwick/Bandage/wiki/Graph-paths"</span><span class="nt" style="color: #000080;">></span>Bandage wiki<span class="nt" style="color: #000080;"></a></span> for details). The example is given below.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

649

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC649" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Let the contig with the name <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>NODE_5_length_100000_cov_215.651<span class="nt" style="color: #000080;"></code></span> consist of the following edges of the assembly graph:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

650

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC650" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"plain"</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">><code</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>    <span class="ni" style="color: #800080;">&gt;</span>EDGE_2_length_33280_cov_199.702</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

651

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<td class="new_line diff-line-num" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

651

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC651" class="line" lang="html">    <span class="ni" style="color: #800080;">&gt;</span>EDGE_5_length_84_cov_321.414"</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

652

</td>

<td class="new_line diff-line-num" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

652

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC652" class="line" lang="html">    <span class="ni" style="color: #800080;">&gt;</span>EDGE_3_length_111_cov_175.304</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

653

</td>

<td class="new_line diff-line-num" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

653

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC653" class="line" lang="html">    <span class="ni" style="color: #800080;">&gt;</span>EDGE_5_length_84_cov_321.414"</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

654

</td>

<td class="new_line diff-line-num" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

654

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC654" class="line" lang="html">    <span class="ni" style="color: #800080;">&gt;</span>EDGE_4_length_66661_cov_223.548</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

655

</td>

<td class="new_line diff-line-num" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

655

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC655" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

656

</td>

<td class="new_line diff-line-num old" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC656" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Then, <span class="nt" style="color: #000080;"><code></span>contigs.paths<span class="nt" style="color: #000080;"></code></span> will contain the following record:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

657

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<td class="new_line diff-line-num old" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC657" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;"><span class="idiff left right deletion" style="background-color: #fac5cd;">><code</span>></span>    NODE_5_length_100000_cov_215.651</span>

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<td class="new_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

656

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC656" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Then, <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>contigs.paths<span class="nt" style="color: #000080;"></code></span> will contain the following record:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

657

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC657" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"plain"</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">><code</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>    NODE_5_length_100000_cov_215.651</span>

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<td class="old_line diff-line-num" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

658

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<td class="new_line diff-line-num" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

658

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC658" class="line" lang="html">    2+,5-,3+,5-,4+</span>

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659

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<td class="new_line diff-line-num" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

659

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC659" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>

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<td class="old_line diff-line-num" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

660

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<td class="new_line diff-line-num" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

660

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC660" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Since the current version of Bandage does not accept paths with gaps, paths corresponding contigs/scaffolds jumping over a gap in the assembly graph are split by semicolon at the gap positions. For example, the following record<span class="nt" style="color: #000080;"></p></span></span>

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661

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<td class="new_line diff-line-num old" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC661" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;"><span class="idiff left right deletion" style="background-color: #fac5cd;">><code</span>></span>    NODE_3_length_237403_cov_243.207</span>

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<td class="old_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

661

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC661" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"plain"</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">><code</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>    NODE_3_length_237403_cov_243.207</span>

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662

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<td class="new_line diff-line-num" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

662

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC662" class="line" lang="html">    21-,17-,15+,17-,16+;</span>

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663

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<td class="new_line diff-line-num" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

663

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC663" class="line" lang="html">    31+,23-,22+,23-,4-</span>

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664

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664

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC664" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>

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665

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<td class="new_line diff-line-num old" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC665" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>states that <span class="nt" style="color: #000080;"><code></span>NODE_3_length_237403_cov_243.207<span class="nt" style="color: #000080;"></code></span> corresponds to the path with 10 edges, but jumps over a gap between edges <span class="nt" style="color: #000080;"><code></span>EDGE_16_length_21503_cov_482.709<span class="nt" style="color: #000080;"></code></span> and <span class="nt" style="color: #000080;"><code></span>EDGE_31_length_140767_cov_220.239<span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>

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665

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC665" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>states that <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>NODE_3_length_237403_cov_243.207<span class="nt" style="color: #000080;"></code></span> corresponds to the path with 10 edges, but jumps over a gap between edges <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>EDGE_16_length_21503_cov_482.709<span class="nt" style="color: #000080;"></code></span> and <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>EDGE_31_length_140767_cov_220.239<span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>

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666

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666

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC666" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"spadesoutput:full"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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667

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667

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC667" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Complete list of output files<span class="nt" style="color: #000080;"></h3></span></span>

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668

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<td class="new_line diff-line-num old" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC668" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The full list of <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> content is presented below:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num new" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

668

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC668" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The full list of <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span> content is presented below:<span class="nt" style="color: #000080;"></p></span></span>

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669

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669

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC669" class="line" lang="html"><span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span></span>

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670

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670

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC670" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span></span>

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671

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671

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC671" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>scaffolds.fasta - resulting scaffolds (recommended for use as resulting sequences)<span class="nt" style="color: #000080;"></p></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -709,18 +709,18 @@ Here <code>3</code> is the number of the contig/scaffold, <code>237403</code> is</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC709" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>K<span class="ni" style="color: #800080;">&lt;</span>##<span class="ni" style="color: #800080;">&gt;</span>/ - directory containing intermediate files from the run with K=<span class="ni" style="color: #800080;">&lt;</span>##<span class="ni" style="color: #800080;">&gt;</span>. These files should not be used as assembly results; use resulting contigs/scaffolds in files mentioned above.<span class="nt" style="color: #000080;"></p></span></span>

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710

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711

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712

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC712" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes will overwrite these files and directories if they exist in the specified <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

712

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC712" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAdes will overwrite these files and directories if they exist in the specified <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

713

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<td class="new_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

713

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC713" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"plasmidout"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

714

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<td class="new_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

714

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC714" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>plasmidSPAdes output<span class="nt" style="color: #000080;"></h2></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

715

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<td class="new_line diff-line-num" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

715

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC715" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>plasmidSPAdes and metaplasmidSPAdes output only DNA sequences from putative plasmids. Output file names and formats remain the same as in SPAdes (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#spadesoutput"</span><span class="nt" style="color: #000080;">></span>previous<span class="nt" style="color: #000080;"></a></span> section), with the following differences.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

716

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<td class="new_line diff-line-num old" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC716" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For all plasmidSPAdes' contig names in <span class="nt" style="color: #000080;"><code></span>contigs.fasta<span class="nt" style="color: #000080;"></code></span>, <span class="nt" style="color: #000080;"><code></span>scaffolds.fasta<span class="nt" style="color: #000080;"></code></span> and <span class="nt" style="color: #000080;"><code></span>assembly_graph.fastg<span class="nt" style="color: #000080;"></code></span> we append suffix <span class="nt" style="color: #000080;"><code></span>_component_X<span class="nt" style="color: #000080;"></code></span>, where <span class="nt" style="color: #000080;"><code></span>X<span class="nt" style="color: #000080;"></code></span> is the id of the putative plasmid, which the contig belongs to. Note that plasmidSPAdes may not be able to separate similar plasmids and thus their contigs may appear with the same id. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

716

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC716" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For all plasmidSPAdes' contig names in <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>contigs.fasta<span class="nt" style="color: #000080;"></code></span>, <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>scaffolds.fasta<span class="nt" style="color: #000080;"></code></span> and <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>assembly_graph.fastg<span class="nt" style="color: #000080;"></code></span> we append suffix <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>_component_X<span class="nt" style="color: #000080;"></code></span>, where <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>X<span class="nt" style="color: #000080;"></code></span> is the id of the putative plasmid, which the contig belongs to. Note that plasmidSPAdes may not be able to separate similar plasmids and thus their contigs may appear with the same id. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

717

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<td class="new_line diff-line-num" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

717

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC717" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"metapv"</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

718

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<td class="new_line diff-line-num" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

718

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC718" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>metaplasmidSPAdes/metaviralSPAdes output<span class="nt" style="color: #000080;"></h2></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

719

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<td class="new_line diff-line-num old" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC719" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The repeat resolution and extrachromosomal element detection in metaplasmidSPAdes/metaviralSPAdes is run independently for different coverage cutoffs values (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.cshlp.org/content/29/6/961.short"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>paper<span class="nt" style="color: #000080;"></a></span> for details). In order to distinguish contigs with putative plasmids detected at different cutoff levels we extend the contig name in FASTA file with cutoff value used for this particular contig (in format <span class="nt" style="color: #000080;"><code></span>_cutoff_N<span class="nt" style="color: #000080;"></code></span>). This is why, in the contrast to regular SPAdes pipeline, there might be a contig with <span class="nt" style="color: #000080;"><code></span>NODE_1_<span class="nt" style="color: #000080;"></code></span> prefix for each cutoff with potential plasmids detected. In following example, there were detected two potential viruses using cutoff 0, one virus was detected with cutoff 5 and one with cutoff 10.<span class="nt" style="color: #000080;"><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

719

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC719" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The repeat resolution and extrachromosomal element detection in metaplasmidSPAdes/metaviralSPAdes is run independently for different coverage cutoffs values (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://genome.cshlp.org/content/29/6/961.short"</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"nofollow"</span><span class="nt" style="color: #000080;">></span>paper<span class="nt" style="color: #000080;"></a></span> for details). In order to distinguish contigs with putative plasmids detected at different cutoff levels we extend the contig name in FASTA file with cutoff value used for this particular contig (in format <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>_cutoff_N<span class="nt" style="color: #000080;"></code></span>). This is why, in the contrast to regular SPAdes pipeline, there might be a contig with <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>NODE_1_<span class="nt" style="color: #000080;"></code></span> prefix for each cutoff with potential plasmids detected. In following example, there were detected two potential viruses using cutoff 0, one virus was detected with cutoff 5 and one with cutoff 10.<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

720

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<td class="new_line diff-line-num" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

720

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC720" class="line" lang="html">Also, we add a suffix that shows the structure of the suspective extrachromosomal element.<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

721

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<td class="new_line diff-line-num" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

721

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC721" class="line" lang="html">For metaplasmid mode we output only circular putative plasmids.<span class="nt" style="color: #000080;"><br></span></span>

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<td class="old_line diff-line-num" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

722

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<td class="new_line diff-line-num" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

722

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC722" class="line" lang="html">For metaviral mode we also output linear putative viruses and linear viruses with simple repeats ('9'-shaped components in the assembly graph) sequences.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

723

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<td class="new_line diff-line-num old" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC723" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"plain"</span><span class="nt" style="color: #000080;"><span class="idiff left right deletion" style="background-color: #fac5cd;">><code</span>></span><span class="ni" style="color: #800080;">&gt;</span>NODE_1_length_40003_cov_13.48_cutoff_0_type_circular</span>

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<td class="old_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

723

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC723" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"plain"</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">><code</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&gt;</span>NODE_1_length_40003_cov_13.48_cutoff_0_type_circular</span>

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<td class="old_line diff-line-num" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

724

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<td class="new_line diff-line-num" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

724

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC724" class="line" lang="html"><span class="ni" style="color: #800080;">&gt;</span>NODE_2_length_30000_cov_4.20_cutoff_0_type_linear</span>

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<td class="old_line diff-line-num" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

725

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<td class="new_line diff-line-num" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

725

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC725" class="line" lang="html"><span class="ni" style="color: #800080;">&gt;</span>NODE_1_length_20000_cov_20.42_cutoff_5_type_circular</span>

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<td class="old_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

726

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<td class="new_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

726

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC726" class="line" lang="html"><span class="ni" style="color: #800080;">&gt;</span>NODE_1_length_10000_cov_198.4_cutoff_10_type_linearrepeat</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -729,7 +729,7 @@ For metaviral mode we also output linear putative viruses and linear viruses wit</td>

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729

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC729" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>biosyntheticSPAdes output<span class="nt" style="color: #000080;"></h2></span></span>

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730

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC730" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>biosyntheticSPAdes outputs four files of interest:<span class="nt" style="color: #000080;"></p></span></span>

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731

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC731" class="line" lang="html"><span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="old_line diff-line-num old" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

732

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<td class="new_line diff-line-num old" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC732" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>scaffolds.fasta – contains DNA sequences from putative biosynthetic gene clusters (BGC). Since each sample may contain multiple BGCs and biosyntheticSPAdes can output several putative DNA sequences for eash cluster, for each contig name we append suffix <span class="nt" style="color: #000080;"><code></span>_cluster_X_candidate_Y<span class="nt" style="color: #000080;"></code></span>, where X is the id of the BGC and Y is the id of the candidate from the BGC.<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num new" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC732" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>scaffolds.fasta – contains DNA sequences from putative biosynthetic gene clusters (BGC). Since each sample may contain multiple BGCs and biosyntheticSPAdes can output several putative DNA sequences for eash cluster, for each contig name we append suffix <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>_cluster_X_candidate_Y<span class="nt" style="color: #000080;"></code></span>, where X is the id of the BGC and Y is the id of the candidate from the BGC.<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

733

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<td class="new_line diff-line-num" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

733

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC733" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>raw_scaffolds.fasta – SPAdes scaffolds generated without domain-graph related algorithms. Very close to regular scaffolds.fasta file.<span class="nt" style="color: #000080;"></li></span></span>

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<td class="old_line diff-line-num" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

734

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<td class="new_line diff-line-num" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

734

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC734" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>hmm_statistics.txt – contains statistics about BGC composition in the sample. First, it outputs number of domain hits in the sample. Then, for each BGC candidate we output domain order with positions on the corresponding DNA sequence from scaffolds.fasta.<span class="nt" style="color: #000080;"></li></span></span>

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735

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<td class="new_line diff-line-num" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

735

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC735" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>domain_graph.dot – contains domain graph structure, that can be used to assess complexity of the sample and structure of BGCs. For more information about domain graph construction, please refer to the paper.<span class="nt" style="color: #000080;"></li></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -742,7 +742,7 @@ For metaviral mode we also output linear putative viruses and linear viruses wit</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC742" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Stand-alone binaries released within SPAdes package<span class="nt" style="color: #000080;"></h1></span></span>

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743

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC743" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec4.1"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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744

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<td class="new_line diff-line-num" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

744

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC744" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>k-mer counting<span class="nt" style="color: #000080;"></h2></span></span>

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<td class="old_line diff-line-num old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

745

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<td class="new_line diff-line-num old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC745" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To provide input data to SPAdes k-mer counting tool <span class="nt" style="color: #000080;"><code></span>spades-kmercounter <span class="nt" style="color: #000080;"></code></span> you may just specify files in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec3.1"</span><span class="nt" style="color: #000080;">></span>SPAdes-supported formats<span class="nt" style="color: #000080;"></a></span> without any flags (after all options) or provide dataset description file in YAML format.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC745" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To provide input data to SPAdes k-mer counting tool <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-kmercounter <span class="nt" style="color: #000080;"></code></span> you may just specify files in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec3.1"</span><span class="nt" style="color: #000080;">></span>SPAdes-supported formats<span class="nt" style="color: #000080;"></a></span> without any flags (after all options) or provide dataset description file in YAML format.<span class="nt" style="color: #000080;"></p></span></span>

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746

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746

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC746" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Output: <span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span>/final_kmers - unordered set of kmers in binary format. Kmers from both forward a<span class="nt" style="color: #000080;"><br></span></span>

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747

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747

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC747" class="line" lang="html">nd reverse-complementary reads are taken into account.<span class="nt" style="color: #000080;"></p></span></span>

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748

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<td class="new_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

748

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC748" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Output format: All kmers are written sequentially without any separators. Each kmer takes the same nu<span class="nt" style="color: #000080;"><br></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -750,7 +750,7 @@ mber of bits. One kmer of length K takes 2*K bits. Kmers are aligned by 64 bits.</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC750" class="line" lang="html">r with length=21 takes 8 bytes, with length=33 takes 16 bytes, and with length=55 takes 16 bytes. Eac<span class="nt" style="color: #000080;"><br></span></span>

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751

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<td class="new_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC751" class="line" lang="html">h nucleotide is coded with 2 bits: 00 - A, 01 - C, 10 - G, 11 - T.<span class="nt" style="color: #000080;"></p></span></span>

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752

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC752" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Example:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

753

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<td class="new_line diff-line-num old" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC753" class="line" lang="html"><span class="nt" style="color: #000080;"><pre<span class="idiff left right deletion" style="background-color: #fac5cd;">><code</span>></span>    For kmer: AGCTCT</span>

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<td class="old_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

753

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC753" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;"><span class="idiff addition" style="background-color: #c7f0d2;">><code</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>    For kmer: AGCTCT</span>

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754

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<td class="new_line diff-line-num" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC754" class="line" lang="html">    Memory: 6 bits * 2 = 12, 64 bits (8 bytes)</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC755" class="line" lang="html">    Let’s describe bytes:</span>

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756

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756

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC756" class="line" lang="html">    data[0] = AGCT -<span class="ni" style="color: #800080;">&gt;</span> 11 01 10 00 -<span class="ni" style="color: #800080;">&gt;</span> 0xd8                                </span>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -762,103 +762,103 @@ h nucleotide is coded with 2 bits: 00 - A, 01 - C, 10 - G, 11 - T.</p></td>

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762

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC762" class="line" lang="html">    data[6] = 0000 -<span class="ni" style="color: #800080;">&gt;</span> 00 00 00 00 -<span class="ni" style="color: #800080;">&gt;</span> 0x00</span>

</pre></td>

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763

</td>

<td class="new_line diff-line-num" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

763

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC763" class="line" lang="html">    data[7] = 0000 -<span class="ni" style="color: #800080;">&gt;</span> 00 00 00 00 -<span class="ni" style="color: #800080;">&gt;</span> 0x00</span>

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<td class="old_line diff-line-num" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

764

</td>

<td class="new_line diff-line-num" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

764

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC764" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>

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<td class="old_line diff-line-num old" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

765

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<td class="new_line diff-line-num old" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC765" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code></span>spades-kmercount [OPTION...] <span class="ni" style="color: #800080;">&lt;</span>input files<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

765

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC765" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-kmercount [OPTION...] <span class="ni" style="color: #800080;">&lt;</span>input files<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

766

</td>

<td class="new_line diff-line-num" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

766

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC766" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The options are:<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

767

</td>

<td class="new_line diff-line-num old" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC767" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-d, --dataset file <span class="ni" style="color: #800080;">&lt;</span>file name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

767

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC767" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-d, --dataset file <span class="ni" style="color: #800080;">&lt;</span>file name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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768

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<td class="new_line diff-line-num" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

768

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC768" class="line" lang="html">dataset description (in YAML format), input files ignored<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

769

</td>

<td class="new_line diff-line-num old" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC769" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-k, --kmer <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

769

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC769" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-k, --kmer <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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770

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<td class="new_line diff-line-num" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

770

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC770" class="line" lang="html">k-mer length (default: 21)<span class="nt" style="color: #000080;"></p></span></span>

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771

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<td class="new_line diff-line-num old" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC771" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-t, --threads <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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771

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC771" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-t, --threads <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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772

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772

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC772" class="line" lang="html">number of threads to use (default: number of CPUs)<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

773

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<td class="new_line diff-line-num old" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC773" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-w, --workdir <span class="ni" style="color: #800080;">&lt;</span>dir name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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773

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC773" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-w, --workdir <span class="ni" style="color: #800080;">&lt;</span>dir name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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774

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<td class="new_line diff-line-num" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

774

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC774" class="line" lang="html">working directory to use (default: current directory)<span class="nt" style="color: #000080;"></p></span></span>

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775

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<td class="new_line diff-line-num old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC775" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-b, --bufsize <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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775

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC775" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-b, --bufsize <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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776

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776

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC776" class="line" lang="html">sorting buffer size in bytes, per thread (default 536870912)<span class="nt" style="color: #000080;"></p></span></span>

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777

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<td class="new_line diff-line-num old" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC777" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-h, --help <span class="nt" style="color: #000080;"></code><br></span></span>

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777

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC777" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-h, --help <span class="nt" style="color: #000080;"></code><br></span></span>

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778

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC778" class="line" lang="html">print help message<span class="nt" style="color: #000080;"></p></span></span>

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779

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779

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC779" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec4.2"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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780

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780

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC780" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>k-mer coverage read filter<span class="nt" style="color: #000080;"></h2></span></span>

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<td class="old_line diff-line-num old" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

781

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<td class="new_line diff-line-num old" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC781" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>spades-read-filter<span class="nt" style="color: #000080;"></code></span> is a tool for filtering reads with median kmer coverage less than threshold.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

782

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<td class="new_line diff-line-num old" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC782" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To provide input data to SPAdes k-mer read filter tool <span class="nt" style="color: #000080;"><code></span>spades-read-filter <span class="nt" style="color: #000080;"></code></span> you should provide dataset description file in YAML format.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

783

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<td class="new_line diff-line-num old" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC783" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code></span>spades-read-filter [OPTION...] -d <span class="ni" style="color: #800080;">&lt;</span>yaml<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

781

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC781" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-read-filter<span class="nt" style="color: #000080;"></code></span> is a tool for filtering reads with median kmer coverage less than threshold.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

782

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC782" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To provide input data to SPAdes k-mer read filter tool <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-read-filter <span class="nt" style="color: #000080;"></code></span> you should provide dataset description file in YAML format.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

783

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC783" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-read-filter [OPTION...] -d <span class="ni" style="color: #800080;">&lt;</span>yaml<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

784

</td>

<td class="new_line diff-line-num" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

784

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC784" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The options are:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

785

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<td class="new_line diff-line-num old" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC785" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-d, --dataset file <span class="ni" style="color: #800080;">&lt;</span>file name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

785

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC785" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-d, --dataset file <span class="ni" style="color: #800080;">&lt;</span>file name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

786

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<td class="new_line diff-line-num" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

786

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC786" class="line" lang="html">dataset description (in YAML format)<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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787

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<td class="new_line diff-line-num old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC787" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-k, --kmer <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC787" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-k, --kmer <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC788" class="line" lang="html">k-mer length (default: 21)<span class="nt" style="color: #000080;"></p></span></span>

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789

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<td class="new_line diff-line-num old" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC789" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-t, --threads <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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789

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC789" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-t, --threads <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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790

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC790" class="line" lang="html">number of threads to use (default: number of CPUs)<span class="nt" style="color: #000080;"></p></span></span>

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791

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<td class="new_line diff-line-num old" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC791" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-o, --outdir <span class="ni" style="color: #800080;">&lt;</span>dir<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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791

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC791" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-o, --outdir <span class="ni" style="color: #800080;">&lt;</span>dir<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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792

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC792" class="line" lang="html">output directory to use (default: current directory)<span class="nt" style="color: #000080;"></p></span></span>

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793

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<td class="new_line diff-line-num old" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC793" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-c, --cov <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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793

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC793" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-c, --cov <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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794

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794

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC794" class="line" lang="html">median kmer count threshold (read pairs, s.t. kmer count median for BOTH reads LESS OR EQUAL to this value will be ignored)<span class="nt" style="color: #000080;"></p></span></span>

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795

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</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC795" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-h, --help <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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795

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC795" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-h, --help <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

796

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<td class="new_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

796

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC796" class="line" lang="html">print help message<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

797

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<td class="new_line diff-line-num" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

797

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC797" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec4.3"</span><span class="nt" style="color: #000080;">></a></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

798

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<td class="new_line diff-line-num" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

798

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC798" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>k-mer cardinality estimating<span class="nt" style="color: #000080;"></h2></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

799

</td>

<td class="new_line diff-line-num old" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC799" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>spades-kmer-estimating <span class="nt" style="color: #000080;"></code></span> is a tool for estimating approximate number of unique k-mers in the provided reads. Kmers from reverse-complementary reads aren"t taken into account for k-mer cardinality estimating.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

800

</td>

<td class="new_line diff-line-num old" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC800" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To provide input data to SPAdes k-mer cardinality estimating tool <span class="nt" style="color: #000080;"><code></span>spades-kmer-estimating <span class="nt" style="color: #000080;"></code></span> you should provide dataset description file in YAML format.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

801

</td>

<td class="new_line diff-line-num old" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC801" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code></span>spades-kmer-estimating [OPTION...] -d <span class="ni" style="color: #800080;">&lt;</span>yaml<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

799

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC799" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-kmer-estimating <span class="nt" style="color: #000080;"></code></span> is a tool for estimating approximate number of unique k-mers in the provided reads. Kmers from reverse-complementary reads aren"t taken into account for k-mer cardinality estimating.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

800

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC800" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>To provide input data to SPAdes k-mer cardinality estimating tool <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-kmer-estimating <span class="nt" style="color: #000080;"></code></span> you should provide dataset description file in YAML format.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

801

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC801" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-kmer-estimating [OPTION...] -d <span class="ni" style="color: #800080;">&lt;</span>yaml<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

802

</td>

<td class="new_line diff-line-num" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

802

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC802" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>The options are:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

803

</td>

<td class="new_line diff-line-num old" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC803" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-d, --dataset file <span class="ni" style="color: #800080;">&lt;</span>file name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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803

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC803" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-d, --dataset file <span class="ni" style="color: #800080;">&lt;</span>file name<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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804

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804

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC804" class="line" lang="html">dataset description (in YAML format)<span class="nt" style="color: #000080;"></p></span></span>

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805

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</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC805" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-k, --kmer <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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805

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC805" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-k, --kmer <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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806

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806

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC806" class="line" lang="html">k-mer length (default: 21)<span class="nt" style="color: #000080;"></p></span></span>

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807

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<td class="new_line diff-line-num old" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC807" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-t, --threads <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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807

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC807" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-t, --threads <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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808

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808

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC808" class="line" lang="html">number of threads to use (default: number of CPUs)<span class="nt" style="color: #000080;"></p></span></span>

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809

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC809" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-h, --help <span class="nt" style="color: #000080;"></code><br></span></span>

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809

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC809" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-h, --help <span class="nt" style="color: #000080;"></code><br></span></span>

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810

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810

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC810" class="line" lang="html">print help message<span class="nt" style="color: #000080;"></p></span></span>

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811

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811

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC811" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec4.4"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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812

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812

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC812" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Graph construction<span class="nt" style="color: #000080;"></h2></span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

813

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<td class="new_line diff-line-num old" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC813" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Graph construction tool <span class="nt" style="color: #000080;"><code></span>spades-gbuilder <span class="nt" style="color: #000080;"></code></span> has two mandatory options: dataset description file in YAML format and an output file name.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

814

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<td class="new_line diff-line-num old" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC814" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code></span>spades-gbuilder <span class="ni" style="color: #800080;">&lt;</span>dataset description (in YAML)<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>output filename<span class="ni" style="color: #800080;">&gt;</span> [-k <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-t <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-tmpdir <span class="ni" style="color: #800080;">&lt;</span>dir<span class="ni" style="color: #800080;">&gt;</span>] [-b <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-unitigs|-fastg|-gfa|-spades]<span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

813

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC813" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Graph construction tool <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-gbuilder <span class="nt" style="color: #000080;"></code></span> has two mandatory options: dataset description file in YAML format and an output file name.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

814

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC814" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-gbuilder <span class="ni" style="color: #800080;">&lt;</span>dataset description (in YAML)<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>output filename<span class="ni" style="color: #800080;">&gt;</span> [-k <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-t <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-tmpdir <span class="ni" style="color: #800080;">&lt;</span>dir<span class="ni" style="color: #800080;">&gt;</span>] [-b <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-unitigs|-fastg|-gfa|-spades]<span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

815

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<td class="new_line diff-line-num" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

815

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC815" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Additional options are:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

816

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<td class="new_line diff-line-num old" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC816" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-k <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

816

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC816" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-k <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

817

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<td class="new_line diff-line-num" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

817

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC817" class="line" lang="html">k-mer length used for construction (must be odd)<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

818

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<td class="new_line diff-line-num old" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC818" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-t <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

818

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC818" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-t <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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819

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<td class="new_line diff-line-num" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

819

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC819" class="line" lang="html">number of threads<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

820

</td>

<td class="new_line diff-line-num old" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC820" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-tmp-dir <span class="ni" style="color: #800080;">&lt;</span>dir_name<span class="ni" style="color: #800080;">&gt;</span>  <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

820

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC820" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-tmp-dir <span class="ni" style="color: #800080;">&lt;</span>dir_name<span class="ni" style="color: #800080;">&gt;</span>  <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

821

</td>

<td class="new_line diff-line-num" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

821

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC821" class="line" lang="html">scratch directory to use<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

822

</td>

<td class="new_line diff-line-num old" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC822" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-b <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

822

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC822" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-b <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

823

</td>

<td class="new_line diff-line-num" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

823

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC823" class="line" lang="html">sorting buffer size (per thread, in bytes)<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

824

</td>

<td class="new_line diff-line-num old" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC824" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-unitigs <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

824

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC824" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-unitigs <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

825

</td>

<td class="new_line diff-line-num" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

825

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC825" class="line" lang="html">k-mer length used for construction (must be odd)<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

826

</td>

<td class="new_line diff-line-num old" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC826" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-fastg <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

826

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC826" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-fastg <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

827

</td>

<td class="new_line diff-line-num" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

827

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC827" class="line" lang="html">output graph in FASTG format<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

828

</td>

<td class="new_line diff-line-num old" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC828" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-gfa <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

828

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC828" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-gfa <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

829

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<td class="new_line diff-line-num" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

829

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC829" class="line" lang="html">output graph in GFA1 format<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

830

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<td class="new_line diff-line-num old" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC830" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-spades <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

830

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC830" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-spades <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

831

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<td class="new_line diff-line-num" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

831

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC831" class="line" lang="html">output graph in SPAdes internal format<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

832

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<td class="new_line diff-line-num" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

832

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC832" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec4.5"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

833

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<td class="new_line diff-line-num" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

833

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC833" class="line" lang="html"><span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Long read to graph alignment<span class="nt" style="color: #000080;"></h2></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

834

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<td class="new_line diff-line-num" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

834

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC834" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec4.5.1"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

835

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<td class="new_line diff-line-num" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

835

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC835" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>hybridSPAdes aligner<span class="nt" style="color: #000080;"></h3></span></span>

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<td class="old_line diff-line-num old" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

836

</td>

<td class="new_line diff-line-num old" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC836" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>A tool <span class="nt" style="color: #000080;"><code></span>spades-gmapper <span class="nt" style="color: #000080;"></code></span> gives opportunity to extract long read alignments generated with hybridSPAdes pipeline options. It has three mandatory options: dataset description file in YAML format, graph file in GFA format and an output file name.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

837

</td>

<td class="new_line diff-line-num old" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC837" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code></span>spades-gmapper <span class="ni" style="color: #800080;">&lt;</span>dataset description (in YAML)<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>graph (in GFA)<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>output filename<span class="ni" style="color: #800080;">&gt;</span> [-k <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-t <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-tmpdir <span class="ni" style="color: #800080;">&lt;</span>dir<span class="ni" style="color: #800080;">&gt;</span>]<span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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836

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC836" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>A tool <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-gmapper <span class="nt" style="color: #000080;"></code></span> gives opportunity to extract long read alignments generated with hybridSPAdes pipeline options. It has three mandatory options: dataset description file in YAML format, graph file in GFA format and an output file name.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

837

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC837" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-gmapper <span class="ni" style="color: #800080;">&lt;</span>dataset description (in YAML)<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>graph (in GFA)<span class="ni" style="color: #800080;">&gt;</span> <span class="ni" style="color: #800080;">&lt;</span>output filename<span class="ni" style="color: #800080;">&gt;</span> [-k <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-t <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-tmpdir <span class="ni" style="color: #800080;">&lt;</span>dir<span class="ni" style="color: #800080;">&gt;</span>]<span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

838

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<td class="new_line diff-line-num" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

838

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC838" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Additional options are:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

839

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<td class="new_line diff-line-num old" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC839" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-k <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

839

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC839" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-k <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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840

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<td class="new_line diff-line-num" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

840

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC840" class="line" lang="html">k-mer length that was used for graph construction<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

841

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<td class="new_line diff-line-num old" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC841" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-t <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

841

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC841" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-t <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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842

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<td class="new_line diff-line-num" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

842

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC842" class="line" lang="html">number of threads<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

843

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<td class="new_line diff-line-num old" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC843" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-tmpdir <span class="ni" style="color: #800080;">&lt;</span>dir_name<span class="ni" style="color: #800080;">&gt;</span>  <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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843

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC843" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-tmpdir <span class="ni" style="color: #800080;">&lt;</span>dir_name<span class="ni" style="color: #800080;">&gt;</span>  <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

844

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<td class="new_line diff-line-num" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

844

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC844" class="line" lang="html">scratch directory to use<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num old" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

845

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<td class="new_line diff-line-num old" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC845" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>While <span class="nt" style="color: #000080;"><code></span>spades-mapper<span class="nt" style="color: #000080;"></code></span> is a solution for those who work on hybridSPAdes assembly and want to get exactly its intermediate results, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec4.5.2"</span><span class="nt" style="color: #000080;">></span>SPAligner<span class="nt" style="color: #000080;"></a></span> is an end-product application for sequence-to-graph alignment with tunable parameters and output types.<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC845" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>While <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades-mapper<span class="nt" style="color: #000080;"></code></span> is a solution for those who work on hybridSPAdes assembly and want to get exactly its intermediate results, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#sec4.5.2"</span><span class="nt" style="color: #000080;">></span>SPAligner<span class="nt" style="color: #000080;"></a></span> is an end-product application for sequence-to-graph alignment with tunable parameters and output types.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC846" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec4.5.2"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

847

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<td class="new_line diff-line-num" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC847" class="line" lang="html"><span class="nt" style="color: #000080;"><h3</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>SPAligner<span class="nt" style="color: #000080;"></h3></span></span>

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<td class="old_line diff-line-num" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

848

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<td class="new_line diff-line-num" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC848" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>A tool for fast and accurate alignment of nucleotide sequences to assembly graphs. It takes file with sequences (in fasta/fastq format) and assembly in GFA format and outputs long read to graph alignment in various formats (such as tsv, fasta and <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/ocxtal/gpa"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"GPA-format spec"</span><span class="nt" style="color: #000080;">></span>GPA<span class="nt" style="color: #000080;"></a></span>).<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC849" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code></span>spaligner assembly/src/projects/spaligner_config.yaml -d <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span> -s <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span> -g <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span> -k <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span> [-t <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-o <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>]<span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC849" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Synopsis: <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spaligner assembly/src/projects/spaligner_config.yaml -d <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span> -s <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span> -g <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span> -k <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span> [-t <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>] [-o <span class="ni" style="color: #800080;">&lt;</span>value<span class="ni" style="color: #800080;">&gt;</span>]<span class="nt" style="color: #000080;"></code></p></span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC850" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Parameters are:<span class="nt" style="color: #000080;"></p></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

851

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<td class="new_line diff-line-num old" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC851" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-d <span class="ni" style="color: #800080;">&lt;</span>type<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

851

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC851" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-d <span class="ni" style="color: #800080;">&lt;</span>type<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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852

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852

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC852" class="line" lang="html">long reads type: nanopore, pacbio<span class="nt" style="color: #000080;"></p></span></span>

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853

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<td class="new_line diff-line-num old" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC853" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-s <span class="ni" style="color: #800080;">&lt;</span>filename<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

853

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC853" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-s <span class="ni" style="color: #800080;">&lt;</span>filename<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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854

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<td class="new_line diff-line-num" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

854

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC854" class="line" lang="html">file with sequences (in fasta/fastq)<span class="nt" style="color: #000080;"></p></span></span>

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855

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<td class="new_line diff-line-num old" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC855" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-g <span class="ni" style="color: #800080;">&lt;</span>filename<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

855

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC855" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-g <span class="ni" style="color: #800080;">&lt;</span>filename<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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856

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<td class="new_line diff-line-num" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

856

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC856" class="line" lang="html">file with graph (in GFA)<span class="nt" style="color: #000080;"></p></span></span>

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857

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<td class="new_line diff-line-num old" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC857" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-k <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

857

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC857" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-k <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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858

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<td class="new_line diff-line-num" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

858

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC858" class="line" lang="html">k-mer length that was used for graph construction<span class="nt" style="color: #000080;"></p></span></span>

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859

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<td class="new_line diff-line-num old" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC859" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-t <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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859

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC859" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-t <span class="ni" style="color: #800080;">&lt;</span>int<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

</pre></td>

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860

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<td class="new_line diff-line-num" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

860

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC860" class="line" lang="html">number of threads (default: 8)<span class="nt" style="color: #000080;"></p></span></span>

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861

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC861" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code></span>-o, --outdir <span class="ni" style="color: #800080;">&lt;</span>dir<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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<td class="old_line diff-line-num new" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

861

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC861" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>-o, --outdir <span class="ni" style="color: #800080;">&lt;</span>dir<span class="ni" style="color: #800080;">&gt;</span> <span class="nt" style="color: #000080;"></code><br></span></span>

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862

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<td class="new_line diff-line-num" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

862

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC862" class="line" lang="html">output directory to use (default: spaligner_result/)<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

863

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<td class="new_line diff-line-num" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC863" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>For more information on parameters and options please refer to main SPAligner manual (assembler/src/projects/spaligner/README.md).<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

864

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<td class="new_line diff-line-num" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC864" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Also if you want to align protein sequences please refer to our <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/ablab/spades/releases/tag/spaligner-paper"</span><span class="nt" style="color: #000080;">></span>pre-release version<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -880,5 +880,5 @@ output directory to use (default: spaligner_result/)</p></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC880" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>In addition, we would like to list your publications that use our software on our website. Please email the reference, the name of your lab, department and institution to <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"mailto:spades.support@cab.spbu.ru"</span><span class="nt" style="color: #000080;">></span>spades.support@cab.spbu.ru<span class="nt" style="color: #000080;"></a></p></span></span>

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881

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<td class="new_line diff-line-num" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC881" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sec6"</span><span class="nt" style="color: #000080;">></a></p></span></span>

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<td class="new_line diff-line-num" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC882" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Feedback and bug reports<span class="nt" style="color: #000080;"></h1></span></span>

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<td class="old_line diff-line-num old" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

883

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<td class="new_line diff-line-num old" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC883" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Your comments, bug reports, and suggestions are very welcomed. They will help us to further improve SPAdes. If you have any troubles running SPAdes, please send us <span class="nt" style="color: #000080;"><code></span>params.txt<span class="nt" style="color: #000080;"></code></span> and <span class="nt" style="color: #000080;"><code></span>spades.log<span class="nt" style="color: #000080;"></code></span> from the directory <span class="nt" style="color: #000080;"><code></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>

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<td class="old_line diff-line-num new" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

883

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC883" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>Your comments, bug reports, and suggestions are very welcomed. They will help us to further improve SPAdes. If you have any troubles running SPAdes, please send us <span class="nt" style="color: #000080;"><code</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>params.txt<span class="nt" style="color: #000080;"></code></span> and <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span>spades.log<span class="nt" style="color: #000080;"></code></span> from the directory <span class="nt" style="color: #000080;"><code</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">class=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"notranslate"</span></span><span class="nt" style="color: #000080;">></span><span class="ni" style="color: #800080;">&lt;</span>output_dir<span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>

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884

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC884" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">dir=</span><span class="s" style="color: #d14;">"auto"</span><span class="nt" style="color: #000080;">></span>You can leave your comments and bug reports at <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/ablab/spades/issues"</span><span class="nt" style="color: #000080;">></span>our GitHub repository tracker<span class="nt" style="color: #000080;"></a></span> or sent it via e-mail: <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"mailto:spades.support@cab.spbu.ru"</span><span class="nt" style="color: #000080;">></span>spades.support@cab.spbu.ru<span class="nt" style="color: #000080;"></a></p><br/><br/><br/><br/><br/></span> <span class="nt" style="color: #000080;"></body></span> <span class="nt" style="color: #000080;"></html></span></span></pre></td>

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</li>

<li id="dcd694f38b9d988eef66a5f4f147c3bf07985834">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#dcd694f38b9d988eef66a5f4f147c3bf07985834" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/cmake/pack.cmake</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -12,10 +12,10 @@ set(CPACK_PACKAGE_NAME "SPAdes")</td>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

12

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC12" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CPACK_PACKAGE_VENDOR <span class="s2" style="color: #d14;">"Saint Petersburg State University"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

13

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

13

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC13" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#set(CPACK_PACKAGE_DESCRIPTION_FILE "${SPADES_MAIN_SRC_DIR}/../README")</span></span>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

14

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

14

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CPACK_RESOURCE_FILE_LICENSE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">SPADES_MAIN_SRC_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/../LICENSE"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

15

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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC15" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CPACK_PACKAGE_VERSION <span class="s2" style="color: #d14;">"3.15.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

15

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC15" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CPACK_PACKAGE_VERSION <span class="s2" style="color: #d14;">"3.15.<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

16

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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

16

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC16" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CPACK_PACKAGE_VERSION_MAJOR <span class="s2" style="color: #d14;">"3"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

17

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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

17

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC17" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CPACK_PACKAGE_VERSION_MINOR <span class="s2" style="color: #d14;">"15"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

18

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<td class="new_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC18" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CPACK_PACKAGE_VERSION_PATCH <span class="s2" style="color: #d14;">"<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

18

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC18" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CPACK_PACKAGE_VERSION_PATCH <span class="s2" style="color: #d14;">"<span class="idiff left right addition" style="background-color: #c7f0d2;">5</span>"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

19

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

19

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC19" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CPACK_STRIP_FILES bin/spades-bwa bin/spades-core bin/spades-corrector-core bin/spades-gbuilder bin/spades-gmapper bin/spades-hammer bin/spades-ionhammer bin/spades-kmercount bin/spades-truseq-scfcorrection<span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

20

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

20

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC20" class="line" lang="cmake"></span>

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21

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

21

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC21" class="line" lang="cmake"></span>

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</li>

<li id="2461f718207d4b6e71915c3d925029ccda6cfcb3">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#2461f718207d4b6e71915c3d925029ccda6cfcb3" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/common/assembly_graph/handlers/used_edge_handler.hpp</strong></a>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//***************************************************************************</span></span>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//* Copyright (c) 2022 Saint-Petersburg State University</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//* All Rights Reserved</span></span>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//* See file LICENSE for details.</span></span>

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//****************************************************************************</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#pragma once</span></span>

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "assembly_graph/core/action_handlers.hpp"</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <unordered_map></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC14" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Graph</span><span class="p">></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC15" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">UsedEdgeHandler</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">omnigraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GraphActionHandler</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">></span> <span class="p">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC16" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EdgeId</span> <span class="n" style="color: #333;">EdgeId</span><span class="p">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC17" class="line" lang="cpp"></span>

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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC18" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">EdgeId</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">storage_</span><span class="p">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC19" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">banned_bases_</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC20" class="line" lang="cpp"></span>

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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC21" class="line" lang="cpp">    <span class="nl">public:</span></span>

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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC22" class="line" lang="cpp">        <span class="n" style="color: #333;">UsedEdgeHandler</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">g</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC23" class="line" lang="cpp">                <span class="n" style="color: #333;">omnigraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GraphActionHandler</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="s" style="color: #d14;">"UsedEdgeHandler"</span><span class="p">),</span> <span class="n" style="color: #333;">storage_</span><span class="p">()</span> <span class="p">{</span> <span class="p">}</span></span>

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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC24" class="line" lang="cpp"></span>

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC25" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">HandleAdd</span><span class="p">(</span><span class="n" style="color: #333;">EdgeId</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="k" style="font-weight: 600;">override</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC26" class="line" lang="cpp">            <span class="n" style="color: #333;">storage_</span><span class="p">.</span><span class="n" style="color: #333;">emplace</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC29" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">HandleDelete</span><span class="p">(</span><span class="n" style="color: #333;">EdgeId</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="k" style="font-weight: 600;">override</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC30" class="line" lang="cpp">            <span class="n" style="color: #333;">storage_</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC31" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

32

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC32" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC33" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">HandleMerge</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">EdgeId</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">old_edges</span><span class="p">,</span> <span class="n" style="color: #333;">EdgeId</span> <span class="n" style="color: #333;">new_edge</span><span class="p">)</span> <span class="k" style="font-weight: 600;">override</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

34

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC34" class="line" lang="cpp">            <span class="n" style="color: #333;">DEBUG</span><span class="p">(</span><span class="s" style="color: #d14;">"merging "</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

35

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC35" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

36

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC36" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">EdgeId</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">old_edges</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

37

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC37" class="line" lang="cpp">                <span class="n" style="color: #333;">DEBUG</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">int_id</span><span class="p">());</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

38

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC38" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">storage_</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC39" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">storage_</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC40" class="line" lang="cpp">                    <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC41" class="line" lang="cpp">            <span class="p">}</span></span>

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC42" class="line" lang="cpp">            <span class="n" style="color: #333;">DEBUG</span><span class="p">(</span><span class="s" style="color: #d14;">"into "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">new_edge</span><span class="p">.</span><span class="n" style="color: #333;">int_id</span><span class="p">());</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

43

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC43" class="line" lang="cpp">            <span class="n" style="color: #333;">storage_</span><span class="p">[</span><span class="n" style="color: #333;">new_edge</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sum</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

44

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC44" class="line" lang="cpp">        <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

45

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC45" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

46

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC46" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">HandleGlue</span><span class="p">(</span><span class="n" style="color: #333;">EdgeId</span> <span class="cm" style="color: #998; font-style: italic;">/*new_edge*/</span><span class="p">,</span> <span class="n" style="color: #333;">EdgeId</span> <span class="cm" style="color: #998; font-style: italic;">/*edge1*/</span><span class="p">,</span> <span class="n" style="color: #333;">EdgeId</span> <span class="cm" style="color: #998; font-style: italic;">/*edge2*/</span><span class="p">)</span> <span class="k" style="font-weight: 600;">override</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

47

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC47" class="line" lang="cpp">            <span class="n" style="color: #333;">VERIFY</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

48

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC48" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

49

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC49" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

50

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC50" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">HandleSplit</span><span class="p">(</span><span class="n" style="color: #333;">EdgeId</span> <span class="cm" style="color: #998; font-style: italic;">/*old_edge*/</span><span class="p">,</span> <span class="n" style="color: #333;">EdgeId</span> <span class="cm" style="color: #998; font-style: italic;">/*new_edge_1*/</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

51

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC51" class="line" lang="cpp">                         <span class="n" style="color: #333;">EdgeId</span> <span class="cm" style="color: #998; font-style: italic;">/*new_edge_2*/</span><span class="p">)</span> <span class="k" style="font-weight: 600;">override</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

52

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC52" class="line" lang="cpp">            <span class="n" style="color: #333;">VERIFY</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC53" class="line" lang="cpp">        <span class="p">}</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC54" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC55" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AddUsed</span><span class="p">(</span><span class="n" style="color: #333;">EdgeId</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC56" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">was_used</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

57

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC57" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">storage_</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">);</span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

58

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC58" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">storage_</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>

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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

59

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC59" class="line" lang="cpp">                <span class="n" style="color: #333;">was_used</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

60

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC60" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

61

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC61" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">new_used</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">g</span><span class="p">().</span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC62" class="line" lang="cpp">            <span class="n" style="color: #333;">VERIFY</span><span class="p">(</span><span class="n" style="color: #333;">new_used</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">was_used</span><span class="p">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC63" class="line" lang="cpp">            <span class="n" style="color: #333;">storage_</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_used</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC64" class="line" lang="cpp">            <span class="n" style="color: #333;">banned_bases_</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">new_used</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">was_used</span><span class="p">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC65" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC66" class="line" lang="cpp"></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC67" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">GetUsedLength</span><span class="p">(</span><span class="n" style="color: #333;">EdgeId</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC68" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">storage_</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">);</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC73" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">banned_bases_</span><span class="p">;</span></span>

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<br>

</li>

<li id="6b87519efcf2bfa28c1e019b7d831798dcad0805">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#6b87519efcf2bfa28c1e019b7d831798dcad0805" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/common/modules/alignment/pacbio/gap_filler.hpp</strong></a>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -120,7 +120,7 @@ class GapFiller {</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC120" class="line" lang="cpp">                    <span class="n" style="color: #333;">MappingPoint</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">PathRange</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">range</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">forward</span><span class="p">,</span> <span class="n" style="color: #333;">GraphPosition</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">old_start_pos</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC122" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">debruijn_graph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Graph</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">g_</span><span class="p">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

123

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<td class="new_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC123" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GAlignerConfig</span> <span class="o" style="font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">&</span></span><span class="n" style="color: #333;">cfg_</span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC123" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GAlignerConfig</span> <span class="n" style="color: #333;">cfg_</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

124

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<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC124" class="line" lang="cpp"><span class="p">};</span></span>

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<td class="old_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

125

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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC125" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

126

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<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC126" class="line" lang="cpp"></span>

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<br>

</li>

<li id="f62d3fc9e2b1b443c5e8c8b35bcdd58889b9f02b">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#f62d3fc9e2b1b443c5e8c8b35bcdd58889b9f02b" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/projects/spades/contig_output_stage.cpp</strong></a>

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<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -10,6 +10,7 @@</td>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

10

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "assembly_graph/core/graph.hpp"</span></span>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

11

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

11

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "assembly_graph/paths/bidirectional_path.hpp"</span></span>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

12

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

12

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp"</span></span>

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<td class="old_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "assembly_graph/handlers/used_edge_handler.hpp"</span></span>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

13

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

14

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "modules/path_extend/pe_resolver.hpp"</span></span>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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</td>

<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

15

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "modules/path_extend/pe_utils.hpp"</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

15

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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "io/dataset_support/read_converter.hpp"</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -19,10 +20,11 @@</td>

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC20" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC21" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC22" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">debruijn_graph</span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC23" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">UsedEdges</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">omnigraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UsedEdgeHandler</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC24" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC25" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">LARGE_FRACTION</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.8</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC26" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC25" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">CheckUsedPath</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BidirectionalPath</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">::</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">unordered_set</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;"><</span></span><span class="n" style="color: #333;">Edge<span class="idiff deletion" style="background-color: #fac5cd;">Id</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">></span></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">used_edges</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC27" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">CheckUsedPath</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BidirectionalPath</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">Used</span>Edge<span class="idiff right addition" style="background-color: #c7f0d2;">s</span></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">used_edges</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC28" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">();</span></span>

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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC29" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">used_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC30" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">total_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -30,22 +32,20 @@ bool CheckUsedPath(const path_extend::BidirectionalPath &path, std::unordered_se</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC32" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">path_len</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC33" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">cur_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">At</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

32

</td>

<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

34

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC34" class="line" lang="cpp">        <span class="n" style="color: #333;">total_len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cur_len</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

33

</td>

<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC33" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">used_edges</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">At</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)))</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC34" class="line" lang="cpp">            <span class="n" style="color: #333;">used_len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cur_len</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

35

</td>

<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC35" class="line" lang="cpp">        <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

35

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC35" class="line" lang="cpp">        <span class="n" style="color: #333;">used_len</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">used_edges</span><span class="p">.</span><span class="n" style="color: #333;">GetUsedLength</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">At</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

36

</td>

<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

36

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC36" class="line" lang="cpp">    <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

37

</td>

<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

37

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC37" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

38

</td>

<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

38

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC38" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">path_len</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

39

</td>

<td class="new_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC39" class="line" lang="cpp">        <span class="n" style="color: #333;">used_edges</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">insert</span></span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">At</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

40

</td>

<td class="new_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC40" class="line" lang="cpp">        <span class="n" style="color: #333;">used_edges</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">insert</span></span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">conjugate</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">At</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)));</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

39

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC39" class="line" lang="cpp">        <span class="n" style="color: #333;">used_edges</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">AddUsed</span></span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">At</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

40

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC40" class="line" lang="cpp">        <span class="n" style="color: #333;">used_edges</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">AddUsed</span></span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">conjugate</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">At</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)));</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

41

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC41" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC42" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//FIXME: constant</span></span>

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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC43" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ge</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">used_len</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">total_len</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">LARGE_FRACTION</span><span class="p">));</span></span>

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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC44" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC45" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC46" class="line" lang="cpp"><span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="n" style="color: #333;">GetCircularScaffolds</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sc_storage</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">::</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">unordered_set</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;"><</span></span><span class="n" style="color: #333;">Edge<span class="idiff deletion" style="background-color: #fac5cd;">Id</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">></span></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">used_edges</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">min_circular_length</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC46" class="line" lang="cpp"><span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="n" style="color: #333;">GetCircularScaffolds</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sc_storage</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">Used</span>Edge<span class="idiff right addition" style="background-color: #c7f0d2;">s</span></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">used_edges</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">min_circular_length</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC47" class="line" lang="cpp">    <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC48" class="line" lang="cpp">    <span class="n" style="color: #333;">INFO</span><span class="p">(</span><span class="s" style="color: #d14;">"Banned "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">used_edges</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" used <span class="idiff left right deletion" style="background-color: #fac5cd;">edg</span>es"</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC48" class="line" lang="cpp">    <span class="n" style="color: #333;">INFO</span><span class="p">(</span><span class="s" style="color: #d14;">"Banned "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">used_edges</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" used <span class="idiff left right addition" style="background-color: #c7f0d2;">bas</span>es"</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC49" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">entry</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sc_storage</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC50" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BidirectionalPath</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC51" class="line" lang="cpp"></span>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -61,7 +61,7 @@ path_extend::PathContainer GetCircularScaffolds(const path_extend::PathContainer</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC61" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC62" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC63" class="line" lang="cpp"></span>

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<td class="new_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC64" class="line" lang="cpp"><span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="n" style="color: #333;">GetTipScaffolds</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sc_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">VertexId</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">forbidden_vertices</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">::</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">unordered_set</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;"><</span></span><span class="n" style="color: #333;">Edge<span class="idiff deletion" style="background-color: #fac5cd;">Id</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">></span></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">used_edges</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">min_linear_length</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC64" class="line" lang="cpp"><span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="n" style="color: #333;">GetTipScaffolds</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sc_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">VertexId</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">forbidden_vertices</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">Used</span>Edge<span class="idiff right addition" style="background-color: #c7f0d2;">s</span></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">used_edges</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">min_linear_length</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC65" class="line" lang="cpp">    <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC66" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">entry</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sc_storage</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC67" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BidirectionalPath</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -211,7 +211,6 @@ void ContigOutput::run(GraphPack &gp, const char*) {</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC211" class="line" lang="cpp">                                                      <span class="n" style="color: #333;">fastg_writer</span><span class="p">));</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC213" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputs_</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">Kind</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PlasmidContigs</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num old" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC214" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">UsedEdges</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">omnigraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SmartContainer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">EdgeId</span><span class="o" style="font-weight: 600;">></span><span class="p">,</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC214" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">gp</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">UsedEdges</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"used_edges"</span><span class="p">))</span></span>

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<td class="new_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC215" class="line" lang="cpp">                    <span class="n" style="color: #333;">gp</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"used_edges"</span><span class="p">,</span> <span class="n" style="color: #333;">UsedEdges</span><span class="p">(</span><span class="n" style="color: #333;">graph</span><span class="p">));</span></span>

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<td class="old_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC216" class="line" lang="cpp">                <span class="n" style="color: #333;">PathContainer</span> <span class="n" style="color: #333;">circulars</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetCircularScaffolds</span><span class="p">(</span><span class="n" style="color: #333;">broken_scaffolds</span><span class="p">,</span> <span class="n" style="color: #333;">gp</span><span class="p">.</span><span class="n" style="color: #333;">get_mutable</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">UsedEdges</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"used_edges"</span><span class="p">),</span> <span class="n" style="color: #333;">cfg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get</span><span class="p">().</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_circular_length</span><span class="p">);</span></span>

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<br>

</li>

<li id="a01bec1175b6b4bf495eef1a6cf54c7ee9a7b3f4">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#a01bec1175b6b4bf495eef1a6cf54c7ee9a7b3f4" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/projects/spades/domain_matcher.cpp</strong></a>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -32,14 +32,20 @@ extern "C" {</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC32" class="line" lang="cpp"></span>

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC33" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">nrps</span> <span class="p">{</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC34" class="line" lang="cpp"></span>

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC35" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">match_contigs_internal</span><span class="p">(</span><span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HMMMatcher</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matcher</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BidirectionalPath</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">path</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC36" class="line" lang="cpp">                                   <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">path_string</span><span class="p">,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC37" class="line" lang="cpp">                                   <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">desc</span><span class="p">,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC38" class="line" lang="cpp">                                   <span class="n" style="color: #333;">ContigAlnInfo</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OFastaReadStream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">oss_contig</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">model_length</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

39

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC39" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">shift</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

40

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC40" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref_shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">GetId</span><span class="p">())</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">shift</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC41" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq_aas</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">translate</span><span class="p">(</span><span class="n" style="color: #333;">path_string</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shift</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC42" class="line" lang="cpp">        <span class="n" style="color: #333;">matcher</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">ref_shift</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">seq_aas</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC35" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">MatchContigsInternal</span><span class="p">(</span><span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HMMMatcher</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matcher</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BidirectionalPath</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">path</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC36" class="line" lang="cpp">                                 <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">path_string</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC37" class="line" lang="cpp">                                 <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">desc</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC38" class="line" lang="cpp">                                 <span class="n" style="color: #333;">ContigAlnInfo</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OFastaReadStream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">oss_contig</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">model_length</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC39" class="line" lang="cpp">                                 <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAA</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC40" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isAA</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC41" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">shift</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC42" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref_shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">GetId</span><span class="p">())</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">shift</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC43" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq_aas</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aa</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">translate</span><span class="p">(</span><span class="n" style="color: #333;">path_string</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shift</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC44" class="line" lang="cpp">            <span class="n" style="color: #333;">matcher</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">ref_shift</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">seq_aas</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC45" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

46

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC46" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC47" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref_shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">GetId</span><span class="p">())</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_0"</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC48" class="line" lang="cpp">            <span class="n" style="color: #333;">matcher</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">ref_shift</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">path_string</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

43

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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC49" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

44

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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC50" class="line" lang="cpp">    <span class="n" style="color: #333;">matcher</span><span class="p">.</span><span class="n" style="color: #333;">summarize</span><span class="p">();</span></span>

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<td class="new_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC51" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -57,8 +63,8 @@ static void match_contigs_internal(hmmer::HMMMatcher &matcher, const path_extend</td>

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC63" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC64" class="line" lang="cpp">            <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC65" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hit</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">()[</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">hit</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">())</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC60" class="line" lang="cpp">            <span class="n" style="color: #333;">seqpos</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqpos</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;"><span class="idiff left right deletion" style="background-color: #fac5cd;">3</span></span>  <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC61" class="line" lang="cpp">            <span class="n" style="color: #333;">seqpos</span><span class="p">.</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqpos</span><span class="p">.</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;"><span class="idiff left right deletion" style="background-color: #fac5cd;">3</span></span>  <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC66" class="line" lang="cpp">            <span class="n" style="color: #333;">seqpos</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqpos</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">*</span> <span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">isAA</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">?</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="mi" style="color: #099;"><span class="idiff addition" style="background-color: #c7f0d2;">3</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="mi" style="color: #099;"><span class="idiff addition" style="background-color: #c7f0d2;">1</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span>  <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC67" class="line" lang="cpp">            <span class="n" style="color: #333;">seqpos</span><span class="p">.</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqpos</span><span class="p">.</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">*</span> <span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">isAA</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">?</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="mi" style="color: #099;"><span class="idiff addition" style="background-color: #c7f0d2;">3</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="mi" style="color: #099;"><span class="idiff addition" style="background-color: #c7f0d2;">1</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span>  <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC68" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC69" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">name</span><span class="p">(</span><span class="n" style="color: #333;">hit</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">());</span></span>

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<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC70" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#pragma omp critical</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -75,30 +81,31 @@ static void match_contigs_internal(hmmer::HMMMatcher &matcher, const path_extend</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC81" class="line" lang="cpp">    <span class="n" style="color: #333;">matcher</span><span class="p">.</span><span class="n" style="color: #333;">reset_top_hits</span><span class="p">();</span></span>

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<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC82" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC83" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC78" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">m</span>atch<span class="idiff right deletion" style="background-color: #fac5cd;">_c</span>ontigs</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">contig_paths</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ScaffoldSequenceMaker</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">scaffold_maker</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC79" class="line" lang="cpp">                         <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HMM</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hmm</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">hmmer_cfg</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cfg</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC80" class="line" lang="cpp">                         <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;">ContigAlnInfo</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OFastaReadStream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">oss_contig</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC84" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">M</span>atch<span class="idiff right addition" style="background-color: #c7f0d2;">C</span>ontigs</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PathContainer</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">contig_paths</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ScaffoldSequenceMaker</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">scaffold_maker</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC85" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HMM</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hmm</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">hmmer_cfg</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cfg</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC86" class="line" lang="cpp">                         <span class="n" style="color: #333;">ContigAlnInfo</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OFastaReadStream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">oss_contig</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC87" class="line" lang="cpp">    <span class="n" style="color: #333;">DEBUG</span><span class="p">(</span><span class="s" style="color: #d14;">"Total contigs: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">contig_paths</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

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<td class="old_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC88" class="line" lang="cpp">    <span class="n" style="color: #333;">DEBUG</span><span class="p">(</span><span class="s" style="color: #d14;">"Model length - "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">());</span></span>

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<td class="old_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC89" class="line" lang="cpp">    <span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HMMMatcher</span> <span class="n" style="color: #333;">matcher</span><span class="p">(</span><span class="n" style="color: #333;">hmm</span><span class="p">,</span> <span class="n" style="color: #333;">cfg</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC90" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">abc</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">eslAMINO</span><span class="p">;</span></span>

</pre></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC91" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">contig_paths</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">contig_paths</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">iter</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

85

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<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC92" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BidirectionalPath</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iter</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">();</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

86

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<td class="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

93

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC93" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">Length</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

87

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<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

94

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC94" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

88

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<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC95" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

89

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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

96

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC96" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">path_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaffold_maker</span><span class="p">.</span><span class="n" style="color: #333;">MakeSequence</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

90

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<td class="new_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC90" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">m</span>atch<span class="idiff deletion" style="background-color: #fac5cd;">_c</span>ontigs<span class="idiff right deletion" style="background-color: #fac5cd;">_i</span>nternal</span><span class="p">(</span><span class="n" style="color: #333;">matcher</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">path_string</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

91

</td>

<td class="new_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC91" class="line" lang="cpp">                             <span class="idiff left right deletion" style="background-color: #fac5cd;">  </span><span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">(),</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">desc</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">desc</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

92

</td>

<td class="new_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC92" class="line" lang="cpp">                             <span class="idiff left right deletion" style="background-color: #fac5cd;">  </span><span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">oss_contig</span><span class="p">,</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">());</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

97

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC97" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">M</span>atch<span class="idiff addition" style="background-color: #c7f0d2;">C</span>ontigs<span class="idiff right addition" style="background-color: #c7f0d2;">I</span>nternal</span><span class="p">(</span><span class="n" style="color: #333;">matcher</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">path_string</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

98

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC98" class="line" lang="cpp">                             <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">(),</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">desc</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">desc</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

99

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC99" class="line" lang="cpp">                             <span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">oss_contig</span><span class="p">,</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()<span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">isAA</span></span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

93

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<td class="new_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

100

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC100" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

94

</td>

<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

101

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC101" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">path_extend</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BidirectionalPath</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">conj_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iter</span><span class="p">.</span><span class="n" style="color: #333;">getConjugate</span><span class="p">();</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

95

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<td class="new_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

102

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC102" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">conj_path</span><span class="p">.</span><span class="n" style="color: #333;">Length</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

96

</td>

<td class="new_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

103

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC103" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

97

</td>

<td class="new_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

104

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC104" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

98

</td>

<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

105

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC105" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">path_string_conj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaffold_maker</span><span class="p">.</span><span class="n" style="color: #333;">MakeSequence</span><span class="p">(</span><span class="n" style="color: #333;">conj_path</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

99

</td>

<td class="new_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC99" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">m</span>atch<span class="idiff deletion" style="background-color: #fac5cd;">_c</span>ontigs<span class="idiff right deletion" style="background-color: #fac5cd;">_i</span>nternal</span><span class="p">(</span><span class="n" style="color: #333;">matcher</span><span class="p">,</span> <span class="n" style="color: #333;">conj_path</span><span class="p">,</span> <span class="n" style="color: #333;">path_string_conj</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

100

</td>

<td class="new_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC100" class="line" lang="cpp">                             <span class="idiff left right deletion" style="background-color: #fac5cd;">  </span><span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">(),</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">desc</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">desc</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

101

</td>

<td class="new_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC101" class="line" lang="cpp">                             <span class="idiff left right deletion" style="background-color: #fac5cd;">  </span><span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">oss_contig</span><span class="p">,</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">());</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

106

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC106" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">M</span>atch<span class="idiff addition" style="background-color: #c7f0d2;">C</span>ontigs<span class="idiff right addition" style="background-color: #c7f0d2;">I</span>nternal</span><span class="p">(</span><span class="n" style="color: #333;">matcher</span><span class="p">,</span> <span class="n" style="color: #333;">conj_path</span><span class="p">,</span> <span class="n" style="color: #333;">path_string_conj</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

107

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC107" class="line" lang="cpp">                             <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">(),</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">desc</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">desc</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

108

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC108" class="line" lang="cpp">                             <span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">oss_contig</span><span class="p">,</span> <span class="n" style="color: #333;">hmm</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()<span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">isAA</span></span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

102

</td>

<td class="new_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

109

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC109" class="line" lang="cpp">    <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC111" class="line" lang="cpp"></span>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -116,10 +123,12 @@ static void ParseHMMFile(std::vector<hmmer::HMM> &hmms, const std::string &filen</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC123" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC124" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC125" class="line" lang="cpp"></span>

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC119" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ParseFASTAFile</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HMM</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hmms</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC120" class="line" lang="cpp">    <span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HMMSequenceBuilder</span> <span class="n" style="color: #333;">builder</span><span class="p">(</span><span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AMINO</span><span class="p">,</span> <span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ScoreSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Default</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC126" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ParseFASTAFile</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HMM</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hmms</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC127" class="line" lang="cpp">                           <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useAA</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC128" class="line" lang="cpp">    <span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HMMSequenceBuilder</span> <span class="n" style="color: #333;">builder</span><span class="p">(</span><span class="n" style="color: #333;">useAA</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AMINO</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DNA</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC129" class="line" lang="cpp">                                      <span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ScoreSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Default</span><span class="p">);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC122" class="line" lang="cpp">    <span class="n" style="color: #333;">ESL_ALPHABET</span>   <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">abc</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">esl_alphabet_Create</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">eslAMINO</span></span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC131" class="line" lang="cpp">    <span class="n" style="color: #333;">ESL_ALPHABET</span>   <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">abc</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">esl_alphabet_Create</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">useAA</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">?</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">eslAMINO</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">eslDNA</span></span><span class="p">);</span></span>

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<td class="new_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC132" class="line" lang="cpp">    <span class="n" style="color: #333;">ESL_SQ</span>         <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qsq</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">esl_sq_CreateDigital</span><span class="p">(</span><span class="n" style="color: #333;">abc</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC133" class="line" lang="cpp">    <span class="n" style="color: #333;">ESL_SQFILE</span>     <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qfp</span>  <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC134" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -138,7 +147,7 @@ static void ParseFASTAFile(std::vector<hmmer::HMM> &hmms, const std::string &fil</td>

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<td class="new_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC147" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC148" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// For each sequence, build a model and save it.</span></span>

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<td class="old_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC149" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">esl_sqio_Read</span><span class="p">(</span><span class="n" style="color: #333;">qfp</span><span class="p">,</span> <span class="n" style="color: #333;">qsq</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">eslOK</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC141" class="line" lang="cpp">        <span class="n" style="color: #333;">INFO</span><span class="p">(</span><span class="s" style="color: #d14;">"Converting "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">qsq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", len: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">qsq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC150" class="line" lang="cpp">        <span class="n" style="color: #333;">INFO</span><span class="p">(</span><span class="s" style="color: #d14;">"Converting "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">useAA</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">?</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"AA"</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"DNA"</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">)</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;"><<</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">" sequence "</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;"><<</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">qsq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", len: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">qsq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC151" class="line" lang="cpp">        <span class="n" style="color: #333;">hmms</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">builder</span><span class="p">.</span><span class="n" style="color: #333;">from_string</span><span class="p">(</span><span class="n" style="color: #333;">qsq</span><span class="p">));</span></span>

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<td class="new_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC152" class="line" lang="cpp">        <span class="n" style="color: #333;">esl_sq_Reuse</span><span class="p">(</span><span class="n" style="color: #333;">qsq</span><span class="p">);</span></span>

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<td class="new_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC153" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -174,14 +183,19 @@ ContigAlnInfo DomainMatcher::MatchDomains(debruijn_graph::GraphPack &gp,</td>

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<td class="new_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC183" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">hmmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HMM</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">hmms</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC184" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">hmm_files</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC185" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ends_with</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">".aa"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ends_with</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">".aa.gz"</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC177" class="line" lang="cpp">            <span class="n" style="color: #333;">ParseFASTAFile</span><span class="p">(</span><span class="n" style="color: #333;">hmms</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC186" class="line" lang="cpp">            <span class="n" style="color: #333;">ParseFASTAFile</span><span class="p">(</span><span class="n" style="color: #333;">hmms</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC187" class="line" lang="cpp">            <span class="n" style="color: #333;">hcfg</span><span class="p">.</span><span class="n" style="color: #333;">E</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hcfg</span><span class="p">.</span><span class="n" style="color: #333;">domE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.01</span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC188" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ends_with</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">".fa"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ends_with</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">".fa.gz"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span></span>

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<td class="old_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC189" class="line" lang="cpp">                   <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ends_with</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">".fna"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ends_with</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">".fna.gz"</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC190" class="line" lang="cpp">            <span class="n" style="color: #333;">ParseFASTAFile</span><span class="p">(</span><span class="n" style="color: #333;">hmms</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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178

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<td class="new_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC191" class="line" lang="cpp">            <span class="n" style="color: #333;">hcfg</span><span class="p">.</span><span class="n" style="color: #333;">E</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hcfg</span><span class="p">.</span><span class="n" style="color: #333;">domE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.01</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

179

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<td class="new_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC192" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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180

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<td class="new_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

193

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC193" class="line" lang="cpp">            <span class="n" style="color: #333;">ParseHMMFile</span><span class="p">(</span><span class="n" style="color: #333;">hmms</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

181

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<td class="new_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

194

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC194" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC195" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

196

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC196" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

184

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<td class="new_line diff-line-num old" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC184" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Setup E-value search space size</span></span>

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<td class="old_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC197" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Setup E-value search space size.  We always use larger size (AA-based),</span></span>

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<td class="old_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

198

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC198" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// so it will be a bit conservative for nucleotide HMMs / sequences</span></span>

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<td class="old_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC199" class="line" lang="cpp">    <span class="n" style="color: #333;">hcfg</span><span class="p">.</span><span class="n" style="color: #333;">Z</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">broken_scaffolds</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

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<td class="old_line diff-line-num" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC200" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC201" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#   pragma omp parallel for</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -193,9 +207,9 @@ ContigAlnInfo DomainMatcher::MatchDomains(debruijn_graph::GraphPack &gp,</td>

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<td class="new_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC207" class="line" lang="cpp">            <span class="n" style="color: #333;">INFO</span><span class="p">(</span><span class="s" style="color: #d14;">"Matching contigs with "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>

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194

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<td class="new_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC208" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC209" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

196

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<td class="new_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC196" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">m</span>atch<span class="idiff right deletion" style="background-color: #fac5cd;">_c</span>ontigs</span><span class="p">(</span><span class="n" style="color: #333;">broken_scaffolds</span><span class="p">,</span> <span class="n" style="color: #333;">scaffold_maker</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

197

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<td class="new_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC197" class="line" lang="cpp">                     <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;">hmms</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">hcfg</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

198

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<td class="new_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC198" class="line" lang="cpp">                     <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;">local_res</span><span class="p">,</span> <span class="n" style="color: #333;">oss_contig</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

210

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC210" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">M</span>atch<span class="idiff right addition" style="background-color: #c7f0d2;">C</span>ontigs</span><span class="p">(</span><span class="n" style="color: #333;">broken_scaffolds</span><span class="p">,</span> <span class="n" style="color: #333;">scaffold_maker</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

211

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC211" class="line" lang="cpp">                     <span class="n" style="color: #333;">hmms</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">hcfg</span><span class="p">,</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

212

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC212" class="line" lang="cpp">                     <span class="n" style="color: #333;">local_res</span><span class="p">,</span> <span class="n" style="color: #333;">oss_contig</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

199

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<td class="new_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

213

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC213" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

200

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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

214

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC214" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#       pragma omp critical</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

201

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<td class="new_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

215

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC215" class="line" lang="cpp">        <span class="p">{</span></span>

</pre></td>

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<br>

</li>

<li id="cae247ed2a05b3b84c463e1573071c9fa168bdbe">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#cae247ed2a05b3b84c463e1573071c9fa168bdbe" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/spades_pipeline/options_parser.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -940,7 +940,9 @@ def add_to_cfg(cfg, log, bin_home, spades_home, args):</td>

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<td class="old_line diff-line-num" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

940

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<td class="new_line diff-line-num" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

940

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC940" class="line" lang="python">        <span class="n" style="color: #333;">hmms</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>

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<td class="old_line diff-line-num" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

941

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<td class="new_line diff-line-num" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

941

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC941" class="line" lang="python">        <span class="n" style="color: #333;">is_hmmfile</span><span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">hmmfile</span><span class="p">:</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">hmmfile</span><span class="p">)</span> \</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

942

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<td class="new_line diff-line-num" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

942

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC942" class="line" lang="python">            <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">hmmfile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"hmm"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">hmmfile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"hmm.gz"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> \</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

943

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<td class="new_line diff-line-num old" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC943" class="line" lang="python">                 <span class="n" style="color: #333;">hmmfile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"aa"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">hmmfile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"aa.gz"</span><span class="p">))</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

943

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC943" class="line" lang="python">                 <span class="n" style="color: #333;">hmmfile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"aa"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">hmmfile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"aa.gz"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> \</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

944

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC944" class="line" lang="python">                 <span class="n" style="color: #333;">hmmfile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"fa"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">hmmfile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"fa.gz"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> \</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

945

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC945" class="line" lang="python">                 <span class="n" style="color: #333;">hmmfile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"fna"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">hmmfile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"fna.gz"</span><span class="p">))</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

944

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<td class="new_line diff-line-num" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

946

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC946" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">hmms_path</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

945

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<td class="new_line diff-line-num" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

947

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC947" class="line" lang="python">            <span class="n" style="color: #333;">hmms</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">","</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">hmms_path</span><span class="p">,</span> <span class="n" style="color: #333;">hmmfile</span><span class="p">)</span></span>

</pre></td>

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946

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<td class="new_line diff-line-num" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC948" class="line" lang="python">                             <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hmmfile</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">hmms_path</span><span class="p">)</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1044,10 +1046,19 @@ def postprocessing(args, cfg, dataset_data, log, spades_home, load_processed_dat</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1046" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">careful</span><span class="p">:</span></span>

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<td class="new_line diff-line-num" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1047" class="line" lang="python">            <span class="n" style="color: #333;">support</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"you cannot specify --careful in RNA-Seq mode!"</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="p">)</span></span>

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1046

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1048

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1048" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1047

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<td class="new_line diff-line-num old" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1047" class="line" lang="python">    <span class="n" style="color: #333;">modes_count</span> <span class="o" style="font-weight: 600;">=</span>  <span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">meta</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">large_genome</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">truseq_mode</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rna</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plasmid</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">single_cell</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isolate</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rnaviral</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1048" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">modes_count</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">([</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">meta</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plasmid</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">meta</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bio</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">meta</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rnaviral</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1049

</td>

<td class="new_line diff-line-num old" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1049" class="line" lang="python">        <span class="n" style="color: #333;">support</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"you cannot simultaneously use more than one mode out of "</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1050

</td>

<td class="new_line diff-line-num old" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1050" class="line" lang="python">                      <span class="s" style="color: #d14;">"Isolate, Metagenomic, Large genome, Illumina TruSeq, RNA-Seq, Plasmid, and Single-cell (except combining Metagenomic and Plasmid)!"</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="p">)</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1049

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1049" class="line" lang="python">    <span class="n" style="color: #333;">modes_count</span> <span class="o" style="font-weight: 600;">=</span>  <span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">large_genome</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rna</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plasmid</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">meta</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">single_cell</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isolate</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rnaviral</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1050

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1050" class="line" lang="python">                    <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">corona</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">metaviral</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">metaplasmid</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bio</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1051

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1051" class="line" lang="python">    <span class="n" style="color: #333;">is_metaplasmid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modes_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">meta</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plasmid</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">metaplasmid</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1052

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1052" class="line" lang="python">    <span class="n" style="color: #333;">is_bgc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modes_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">meta</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bio</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1053

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1053" class="line" lang="python">    <span class="n" style="color: #333;">is_metaviral</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modes_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">meta</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plasmid</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">metaviral</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1054

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1054" class="line" lang="python">    <span class="n" style="color: #333;">is_rnaviral</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modes_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">meta</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rnaviral</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1055

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1055" class="line" lang="python">    <span class="n" style="color: #333;">is_corona</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modes_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">meta</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rnaviral</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">corona</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1056

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1056" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">modes_count</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">is_metaplasmid</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">is_bgc</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">is_metaviral</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">is_rnaviral</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">is_corona</span><span class="p">):</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1057

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1057" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># correct cases:</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1058

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1058" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># - either there is 1 or 0 modes specified</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1059

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1059" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># - or there is 1 of 5 allowed combinations</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1060

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1060" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># everything else is forbidden</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1061

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1061" class="line" lang="python">        <span class="n" style="color: #333;">support</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Specified mode combination is not supported! Check out user manual for available modes."</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1051

</td>

<td class="new_line diff-line-num" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1062

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1062" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">modes_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1052

</td>

<td class="new_line diff-line-num" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1063

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1063" class="line" lang="python">        <span class="n" style="color: #333;">support</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option."</span><span class="p">)</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1053

</td>

<td class="new_line diff-line-num" data-linenumber="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

1064

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1064" class="line" lang="python"></span>

</pre></td>

</tr>

</table>

<br>

</li>

<li id="066017f8828ed241ff09ef4a975cb1f2d4f6be77">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#066017f8828ed241ff09ef4a975cb1f2d4f6be77" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/spades_pipeline/stages/correction_stage.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -10,7 +10,6 @@</td>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

10

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

10

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

11

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

11

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

12

</td>

<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

12

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dir_util</span></span>

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">site</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">addsitedir</span></span>

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC14" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">stages</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">stage</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -71,7 +70,7 @@ class CorrectionIterationStage(stage.Stage):</td>

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<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC70" class="line" lang="python">        <span class="n" style="color: #333;">dst_configs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"configs"</span><span class="p">)</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC71" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">dst_configs</span><span class="p">):</span></span>

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<td class="new_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC72" class="line" lang="python">            <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">dst_configs</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC74" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">dir_util</span></span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"corrector"</span><span class="p">),</span> <span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC73" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">support</span></span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"corrector"</span><span class="p">),</span> <span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC74" class="line" lang="python">        <span class="n" style="color: #333;">cfg_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="s" style="color: #d14;">"corrector.info"</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC75" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC76" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">support</span><span class="p">.</span><span class="n" style="color: #333;">get_tmp_dir</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"corrector_"</span><span class="p">)</span></span>

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<li id="4ca7358cd786dc7d88506f147334f9435130d750">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#4ca7358cd786dc7d88506f147334f9435130d750" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/spades_pipeline/stages/error_correction_stage.py</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -10,7 +10,6 @@</td>

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dir_util</span></span>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">site</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">addsitedir</span></span>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC14" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">commands_parser</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -63,10 +62,10 @@ class ECRunningToolStage(stage.Stage):</td>

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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC62" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">dst_configs</span><span class="p">):</span></span>

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<td class="old_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC63" class="line" lang="python">            <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">dst_configs</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC64" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">iontorrent</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC66" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">dir_util</span></span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"ionhammer"</span><span class="p">),</span> <span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC65" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">support</span></span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"ionhammer"</span><span class="p">),</span> <span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC66" class="line" lang="python">            <span class="n" style="color: #333;">cfg_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="s" style="color: #d14;">"ionhammer.cfg"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC67" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC69" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">dir_util</span></span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"hammer"</span><span class="p">),</span> <span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC68" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">support</span></span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"hammer"</span><span class="p">),</span> <span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC69" class="line" lang="python">            <span class="n" style="color: #333;">cfg_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="s" style="color: #d14;">"config.info"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

71

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<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC70" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC71" class="line" lang="python">        <span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">support</span><span class="p">.</span><span class="n" style="color: #333;">get_tmp_dir</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"hammer_"</span><span class="p">)</span></span>

</pre></td>

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<br>

</li>

<li id="ed083a5a55c9cf1416864acf5c6f9b2612dde905">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#ed083a5a55c9cf1416864acf5c6f9b2612dde905" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/spades_pipeline/stages/pipeline.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -9,8 +9,8 @@</td>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dir_util</span></span>

</pre></td>

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13

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC12" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">support</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">options_storage</span></span>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC15" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Pipeline</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -22,10 +22,10 @@ class Pipeline(object):</td>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC22" class="line" lang="python">            <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC23" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">):</span></span>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC24" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">configs_dir</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC25" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">dir_util</span></span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">configs_dir</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC25" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">support</span></span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">configs_dir</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC26" class="line" lang="python">                                   <span class="n" style="color: #333;">preserve_mode</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC27" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC28" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">dir_util</span></span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">spades_home</span><span class="p">,</span> <span class="s" style="color: #d14;">"configs"</span><span class="p">),</span> <span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC28" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">support</span></span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">spades_home</span><span class="p">,</span> <span class="s" style="color: #d14;">"configs"</span><span class="p">),</span> <span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

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29

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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

29

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC29" class="line" lang="python">                                   <span class="n" style="color: #333;">preserve_mode</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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30

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<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC30" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

31

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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

31

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC31" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">stage</span><span class="p">):</span></span>

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<br>

</li>

<li id="15e14913b0648bc9ab48bd0ffd7e286a964a45b9">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#15e14913b0648bc9ab48bd0ffd7e286a964a45b9" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/spades_pipeline/stages/scaffold_correction_stage.py</strong>

deleted

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

2

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2" class="line" lang="python"></span>

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3

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">############################################################################</span></span>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

4

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015-2019 Saint Petersburg State University</span></span>

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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

5

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2011-2014 Saint Petersburg Academic University</span></span>

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6

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># All Rights Reserved</span></span>

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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

7

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See file LICENSE for details.</span></span>

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC8" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">############################################################################</span></span>

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9

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC9" class="line" lang="python"></span>

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dir_util</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC13" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">commands_parser</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

15

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">options_storage</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">stages</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">stage</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

17

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">process_cfg</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

18

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">process_cfg</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bool_to_str</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

19

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC19" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

20

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># TODO copypast from iteraton stage</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

21

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC21" class="line" lang="python"><span class="n" style="color: #333;">READS_TYPES_USED_IN_CONSTRUCTION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"paired-end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"single"</span><span class="p">,</span> <span class="s" style="color: #d14;">"hq-mate-pairs"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">READS_TYPES_USED_IN_RNA_SEQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"paired-end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"single"</span><span class="p">,</span> <span class="s" style="color: #d14;">"trusted-contigs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"untrusted-contigs"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

23

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC23" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC24" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

25

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">prepare_config_scaffold_correction</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">cfg</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="p">,</span> <span class="n" style="color: #333;">saves_dir</span><span class="p">,</span> <span class="n" style="color: #333;">K</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC26" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC27" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC28" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"K"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">K</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC29" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"dataset"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process_cfg</span><span class="p">.</span><span class="n" style="color: #333;">process_spaces</span><span class="p">(</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">dataset</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC30" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"output_base"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process_cfg</span><span class="p">.</span><span class="n" style="color: #333;">process_spaces</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"SCC"</span><span class="p">))</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC31" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"tmp_dir"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process_cfg</span><span class="p">.</span><span class="n" style="color: #333;">process_spaces</span><span class="p">(</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC32" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"use_additional_contigs"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bool_to_str</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC33" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"main_iteration"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bool_to_str</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC34" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"entry_point"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">BASE_STAGE</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC35" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"load_from"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saves_dir</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC36" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"developer_mode"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bool_to_str</span><span class="p">(</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">developer_mode</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC37" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"max_threads"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">max_threads</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC38" class="line" lang="python">    <span class="n" style="color: #333;">subst_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"max_memory"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">max_memory</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

39

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC39" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

40

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC40" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># todo</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

41

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC41" class="line" lang="python">    <span class="n" style="color: #333;">process_cfg</span><span class="p">.</span><span class="n" style="color: #333;">substitute_params</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">subst_dict</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

42

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC42" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

43

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC43" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC44" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_configs</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">,</span> <span class="n" style="color: #333;">configs_dir</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

45

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC45" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Order matters here!</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

46

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC46" class="line" lang="python">    <span class="n" style="color: #333;">mode_config_mapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">"single_cell"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mda_mode"</span><span class="p">),</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC47" class="line" lang="python">                           <span class="p">(</span><span class="s" style="color: #d14;">"meta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"meta_mode"</span><span class="p">),</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC48" class="line" lang="python">                           <span class="p">(</span><span class="s" style="color: #d14;">"truseq_mode"</span><span class="p">,</span> <span class="s" style="color: #d14;">"moleculo_mode"</span><span class="p">),</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

49

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC49" class="line" lang="python">                           <span class="p">(</span><span class="s" style="color: #d14;">"rna"</span><span class="p">,</span> <span class="s" style="color: #d14;">"rna_mode"</span><span class="p">),</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

50

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC50" class="line" lang="python">                           <span class="p">(</span><span class="s" style="color: #d14;">"large_genome"</span><span class="p">,</span> <span class="s" style="color: #d14;">"large_genome_mode"</span><span class="p">),</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC51" class="line" lang="python">                           <span class="p">(</span><span class="s" style="color: #d14;">"plasmid"</span><span class="p">,</span> <span class="s" style="color: #d14;">"plasmid_mode"</span><span class="p">)]</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

52

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC52" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># ("careful", "careful_mode"),</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

53

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC53" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mode_config_mapping</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

54

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC54" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">mode</span><span class="p">]:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

55

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC55" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"rna"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"meta"</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

56

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC56" class="line" lang="python">                <span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"mda_mode.info"</span><span class="p">))</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

57

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC57" class="line" lang="python">            <span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">configs_dir</span><span class="p">,</span> <span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".info"</span><span class="p">))</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC58" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="s" style="color: #d14;">"careful"</span><span class="p">]:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

59

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC59" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="s" style="color: #d14;">"single_cell"</span><span class="p">]:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC60" class="line" lang="python">            <span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"careful_mda_mode.info"</span><span class="p">))</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

61

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC61" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC62" class="line" lang="python">            <span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"careful_mode.info"</span><span class="p">))</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

63

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC63" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC64" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># special case: extra config</span></span>

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<td class="old_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC65" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rna</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fast</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC66" class="line" lang="python">        <span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"rna_fast_mode.info"</span><span class="p">))</span></span>

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<td class="old_line diff-line-num old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC67" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC68" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC69" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ScaffoldCorrectionStage</span><span class="p">(</span><span class="n" style="color: #333;">stage</span><span class="p">.</span><span class="n" style="color: #333;">Stage</span><span class="p">):</span></span>

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<td class="old_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC70" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">latest</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

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<td class="old_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC71" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">(</span><span class="n" style="color: #333;">ScaffoldCorrectionStage</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">).</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC72" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">latest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">latest</span></span>

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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC73" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC74" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_config</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">cfg</span><span class="p">):</span></span>

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<td class="old_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC75" class="line" lang="python">        <span class="n" style="color: #333;">K</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">iterative_K</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC76" class="line" lang="python">        <span class="n" style="color: #333;">latest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"K%d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">K</span><span class="p">)</span></span>

</pre></td>

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC77" class="line" lang="python">        <span class="n" style="color: #333;">K</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">SCC_K</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC78" class="line" lang="python">        <span class="n" style="color: #333;">data_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"SCC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"K%d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">K</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC79" class="line" lang="python">        <span class="n" style="color: #333;">saves_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"saves"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC80" class="line" lang="python">        <span class="n" style="color: #333;">dst_configs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"configs"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC81" class="line" lang="python">        <span class="n" style="color: #333;">cfg_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="s" style="color: #d14;">"config.info"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC82" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC83" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC84" class="line" lang="python">            <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

85

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC85" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC86" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

87

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC87" class="line" lang="python">        <span class="n" style="color: #333;">dir_util</span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"debruijn"</span><span class="p">),</span> <span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC88" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC89" class="line" lang="python">        <span class="n" style="color: #333;">scaffolds_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">latest</span><span class="p">,</span> <span class="s" style="color: #d14;">"scaffolds.fasta"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC90" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"read_buffer_size"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC91" class="line" lang="python">            <span class="n" style="color: #333;">construction_cfg_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="s" style="color: #d14;">"construction.info"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

92

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC92" class="line" lang="python">            <span class="n" style="color: #333;">process_cfg</span><span class="p">.</span><span class="n" style="color: #333;">substitute_params</span><span class="p">(</span><span class="n" style="color: #333;">construction_cfg_file_name</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"read_buffer_size"</span><span class="p">:</span> <span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">read_buffer_size</span><span class="p">},</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC93" class="line" lang="python">                                          <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC94" class="line" lang="python">        <span class="n" style="color: #333;">process_cfg</span><span class="p">.</span><span class="n" style="color: #333;">substitute_params</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="s" style="color: #d14;">"moleculo_mode.info"</span><span class="p">),</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

95

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC95" class="line" lang="python">                                      <span class="p">{</span><span class="s" style="color: #d14;">"scaffolds_file"</span><span class="p">:</span> <span class="n" style="color: #333;">scaffolds_file</span><span class="p">},</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC96" class="line" lang="python">        <span class="n" style="color: #333;">prepare_config_scaffold_correction</span><span class="p">(</span><span class="n" style="color: #333;">cfg_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">cfg</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">,</span> <span class="n" style="color: #333;">saves_dir</span><span class="p">,</span> <span class="n" style="color: #333;">K</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC97" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC98" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_command</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">cfg</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC99" class="line" lang="python">        <span class="n" style="color: #333;">K</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">SCC_K</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

100

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC100" class="line" lang="python">        <span class="n" style="color: #333;">data_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"SCC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"K%d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">K</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC101" class="line" lang="python">        <span class="n" style="color: #333;">dst_configs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"configs"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC102" class="line" lang="python">        <span class="n" style="color: #333;">cfg_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="s" style="color: #d14;">"config.info"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

103

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC103" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

104

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC104" class="line" lang="python">        <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">cfg_file_name</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

105

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC105" class="line" lang="python">        <span class="n" style="color: #333;">add_configs</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">dst_configs</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

106

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC106" class="line" lang="python">        <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">commands_parser</span><span class="p">.</span><span class="n" style="color: #333;">Command</span><span class="p">(</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

107

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC107" class="line" lang="python">            <span class="n" style="color: #333;">STAGE</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SCC"</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

108

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC108" class="line" lang="python">            <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">bin_home</span><span class="p">,</span> <span class="s" style="color: #d14;">"spades-truseq-scfcorrection"</span><span class="p">),</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

109

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC109" class="line" lang="python">            <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

110

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC110" class="line" lang="python">            <span class="n" style="color: #333;">config_dir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">relpath</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output_dir</span><span class="p">),</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

111

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC111" class="line" lang="python">            <span class="n" style="color: #333;">short_name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">short_name</span><span class="p">)]</span></span>

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<td class="old_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

112

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC112" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">command</span></span></pre></td>

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<br>

</li>

<li id="e7d52fc6222d2879798307c613ccc5ac8e5e671a">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#e7d52fc6222d2879798307c613ccc5ac8e5e671a" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/spades_pipeline/stages/spades_iteration_stage.py</strong></a>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -9,11 +9,11 @@</td>

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>

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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dir_util</span></span>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC12" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">commands_parser</span></span>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">options_storage</span></span>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">stages</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">stage</span></span>

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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">support</span></span>

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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">process_cfg</span></span>

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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">process_cfg</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bool_to_str</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC19" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -139,9 +139,7 @@ class IterationStage(stage.Stage):</td>

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<td class="new_line diff-line-num" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC139" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get_stage</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">short_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">BASE_STAGE</span><span class="p">:</span></span>

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<td class="new_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC140" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">):</span></span>

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<td class="new_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC141" class="line" lang="python">                <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC142" class="line" lang="python"></span>

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<td class="new_line diff-line-num old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC143" class="line" lang="python">            <span class="n" style="color: #333;">dir_util</span><span class="p">.</span><span class="n" style="color: #333;">_path_created</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span>  <span class="c1" style="color: #998; font-style: italic;"># see http://stackoverflow.com/questions/9160227/dir-util-copy-tree-fails-after-shutil-rmtree</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC144" class="line" lang="python">            <span class="n" style="color: #333;">dir_util</span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"debruijn"</span><span class="p">),</span> <span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC142" class="line" lang="python">            <span class="n" style="color: #333;">support</span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"debruijn"</span><span class="p">),</span> <span class="n" style="color: #333;">dst_configs</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC143" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC144" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prev_K</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC145" class="line" lang="python">            <span class="n" style="color: #333;">additional_contigs_dname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"K%d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prev_K</span><span class="p">,</span> <span class="s" style="color: #d14;">"simplified_contigs"</span><span class="p">)</span></span>

</pre></td>

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<br>

</li>

<li id="4ddada5bb56cf32c7e7459698418532494c64c21">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#4ddada5bb56cf32c7e7459698418532494c64c21" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/spades_pipeline/stages/spades_stage.py</strong></a>

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<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -15,7 +15,6 @@ from site import addsitedir</td>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">commands_parser</span></span>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">options_storage</span></span>

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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">stages</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">stage</span></span>

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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">stages</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">scaffold_correction_stage</span></span>

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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">stages</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">spades_iteration_stage</span></span>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">support</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">process_cfg</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">merge_configs</span></span>

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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -325,16 +324,6 @@ class SpadesStage(stage.Stage):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC324" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last_one</span><span class="p">:</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC325" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC326" class="line" lang="python"></span>

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<td class="new_line diff-line-num old" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC328" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">correct_scaffolds</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC329" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">stages</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">scaffold_correction_stage</span><span class="p">.</span><span class="n" style="color: #333;">ScaffoldCorrectionStage</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">latest</span><span class="p">,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC330" class="line" lang="python">                                                                                 <span class="s" style="color: #d14;">"scc"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC331" class="line" lang="python">                                                                                 <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output_files</span><span class="p">,</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC332" class="line" lang="python">                                                                                 <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_configs_dir</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC333" class="line" lang="python">                                                                                 <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">dataset_data</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC334" class="line" lang="python">                                                                                 <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">bin_home</span><span class="p">,</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC335" class="line" lang="python">                                                                                 <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ext_python_modules_home</span><span class="p">,</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC336" class="line" lang="python">                                                                                 <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">python_modules_home</span><span class="p">))</span></span>

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<td class="new_line diff-line-num old" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC337" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">latest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cfg</span><span class="p">.</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"SCC"</span><span class="p">),</span> <span class="s" style="color: #d14;">"K21"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

338

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<td class="new_line diff-line-num" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

327

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC327" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plasmid</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">options_storage</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">meta</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

339

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<td class="new_line diff-line-num" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

328

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC328" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">stages</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">PlasmidGlueFileStage</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">latest</span><span class="p">,</span> <span class="s" style="color: #d14;">"plasmid_copy_files"</span><span class="p">,</span> </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

340

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<td class="new_line diff-line-num" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

329

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC329" class="line" lang="python">                                                    <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output_files</span><span class="p">,</span></span>

</pre></td>

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<br>

</li>

<li id="0109eb8c8746266314fbfa66403f9a857e555a32">

<a href="https://salsa.debian.org/med-team/spades/-/commit/3d6cb8fc3954b52b33a05e4b3b0515a750628653#0109eb8c8746266314fbfa66403f9a857e555a32" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">assembler/src/spades_pipeline/support.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -940,3 +940,30 @@ def is_int(value):</td>

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<td class="old_line diff-line-num" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

940

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<td class="new_line diff-line-num" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

940

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC940" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>

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<td class="old_line diff-line-num" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

941

</td>

<td class="new_line diff-line-num" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

941

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC941" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

942

</td>

<td class="new_line diff-line-num" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">

942

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC942" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

943

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC943" class="line" lang="python"></span>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

944

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC944" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

945

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC945" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># shutil.copyfile does not copy any metadata (time and permission), so one</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

946

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC946" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># cannot expect preserve_mode = False and preserve_times = True to work.</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

947

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC947" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">dst</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_mode</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

948

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC948" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'2'</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

949

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC949" class="line" lang="python">        <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dir_util</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

950

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC950" class="line" lang="python">        <span class="n" style="color: #333;">dir_util</span><span class="p">.</span><span class="n" style="color: #333;">_path_created</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span>  <span class="c1" style="color: #998; font-style: italic;"># see http://stackoverflow.com/questions/9160227/dir-util-copy-tree-fails-after-shutil-rmtree</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

951

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC951" class="line" lang="python">        <span class="n" style="color: #333;">dir_util</span><span class="p">.</span><span class="n" style="color: #333;">copy_tree</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">dst</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_times</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">preserve_times</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_mode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">preserve_mode</span><span class="p">)</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

952

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC952" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

953

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC953" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

954

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC954" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">preserve_mode</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

955

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC955" class="line" lang="python">        <span class="n" style="color: #333;">copy_fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">copyfile</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

956

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC956" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

957

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC957" class="line" lang="python">        <span class="n" style="color: #333;">copy_fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">copy2</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

958

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC958" class="line" lang="python"></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

959

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC959" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">dst</span><span class="p">):</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

960

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC960" class="line" lang="python">        <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">dst</span><span class="p">)</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

961

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC961" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

962

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC962" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># shutil.copytree preserves the timestamp, so we must update it afterwards.</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

963

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC963" class="line" lang="python">    <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">copytree</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">dst</span><span class="p">,</span> <span class="n" style="color: #333;">copy_function</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copy_fn</span><span class="p">)</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

964

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC964" class="line" lang="python"></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

965

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC965" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">preserve_times</span><span class="p">:</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

966

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC966" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">dirpath</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">filenames</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">walk</span><span class="p">(</span><span class="n" style="color: #333;">dst</span><span class="p">):</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

967

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC967" class="line" lang="python">            <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">utime</span><span class="p">(</span><span class="n" style="color: #333;">dirpath</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

968

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC968" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filenames</span><span class="p">:</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

969

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC969" class="line" lang="python">                <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">utime</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dirpath</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">),</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span></pre></td>

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