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<h3>
Andreas Tille pushed to branch manpages
at <a href="https://salsa.debian.org/med-team/bbmap">Debian Med / bbmap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/3758d4c612caa1e1f97bf4d89e5ef85f1f08d4e2">3758d4c6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-04T12:14:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add new manpages and move all manpages into debian/mans subdir
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
debian/createmanpages
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
debian/manpages
</a>
</li>
<li class="file-stats">
<a href="#3a2c34b2b8062d320a25ab1464b4ec79f4952c20">
<span class="new-file">
+
debian/mans/bbduk.sh.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#e48989d0b76f7deb176080cdbf75bd638e725fac">
debian/bbmap.sh.1
→
debian/mans/bbmap.sh.1
</a>
</li>
<li class="file-stats">
<a href="#776b4112df8d10cf7cb1347f0dd6fffea9a7f193">
<span class="new-file">
+
debian/mans/bbnorm.sh.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#c29173014674b2df3174c8a8fd476346903b30fb">
debian/bloomfilter.sh.1
→
debian/mans/bloomfilter.sh.1
</a>
</li>
<li class="file-stats">
<a href="#d864ddf62aef569bfeed5f2b1577c945be7a286c">
<span class="new-file">
+
debian/mans/dedupe.sh.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#b6d717b880589b8f373a3fcb153c36a91c5f439e">
<span class="new-file">
+
debian/mans/reformat.sh.1
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/bbmap/commit/3758d4c612caa1e1f97bf4d89e5ef85f1f08d4e2#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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1
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1
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<td class="diff-line-num new_line 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: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian<span class="idiff left right">/mans</span></span>
</pre>
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<td class="diff-line-num old_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="diff-line-num new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
</pre>
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4
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<td class="diff-line-num new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
4
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
</pre>
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5
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<td class="diff-line-num new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" 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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,6 +24,30 @@ help2man --no-info --no-discard-stderr --help-option=" " \</td>
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<td class="diff-line-num old_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
24
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<td class="diff-line-num new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
24
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
</pre>
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<td class="diff-line-num old_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
25
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<td class="diff-line-num new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<td class="diff-line-num old_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>bbnorm.sh</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Kmer-based error-correction and normalization tool"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>dedupe.sh</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Simplifies assemblies by removing duplicate or contained"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>reformat.sh</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64"</span> <span class="se" style="color: #d14;">\</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>bbduk.sh</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Filters, trims, or masks reads with kmer matches to an artifact/contaminant file"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"></span>
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27
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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28
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"></span>
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29
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/commit/3758d4c612caa1e1f97bf4d89e5ef85f1f08d4e2#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/<span class="idiff left right">mans/</span>*.1</span></pre>
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<li id="3a2c34b2b8062d320a25ab1464b4ec79f4952c20">
<a href="https://salsa.debian.org/med-team/bbmap/commit/3758d4c612caa1e1f97bf4d89e5ef85f1f08d4e2#3a2c34b2b8062d320a25ab1464b4ec79f4952c20"><strong>debian/mans/bbduk.sh.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BBDUK.SH "1" "April 2019" "bbduk.sh 38.43" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">bbduk.sh \- Filters, trims, or masks reads with kmer matches to an artifact/contaminant file</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B bbduk.sh</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,in=<input file> out=<output file> ref=<contaminant files>\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Written by Brian Bushnell</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Last modified March 21, 2019</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Description: Compares reads to the kmers in a reference dataset, optionally</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">allowing an edit distance. Splits the reads into two outputs \- those that</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">match the reference, and those that don't. Can also trim (remove) the matching</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">parts of the reads rather than binning the reads.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Please read bbmap/docs/guides/BBDukGuide.txt for more information.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Input may be stdin or a fasta or fastq file, compressed or uncompressed.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">If you pipe via stdin/stdout, please include the file type; e.g. for gzipped</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">fasta input, set in=stdin.fa.gz</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Input parameters:</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">in=<file> Main input. in=stdin.fq will pipe from stdin.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">in2=<file> Input for 2nd read of pairs in a different file.</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">ref=<file,file> Comma\-delimited list of reference files.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">In addition to filenames, you may also use the keywords:</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">adapters, artifacts, phix, lambda, pjet, mtst, kapa</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">literal=<seq,seq> Comma\-delimited list of literal reference sequences.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">touppercase=f (tuc) Change all bases upper\-case.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">interleaved=auto (int) t/f overrides interleaved autodetection.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">qin=auto Input quality offset: 33 (Sanger), 64, or auto.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">reads=\-1 If positive, quit after processing X reads or pairs.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">copyundefined=f (cu) Process non\-AGCT IUPAC reference bases by making all</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">possible unambiguous copies.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Intended for short motifs</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">or adapter barcodes, as time/memory use is exponential.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">samplerate=1 Set lower to only process a fraction of input reads.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">samref=<file> Optional reference fasta for processing sam files.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Output parameters:</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">out=<file> (outnonmatch) Write reads here that do not contain</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">kmers matching the database.</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">\&'out=stdout.fq' will pipe</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.IP</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">to standard out.</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.PP</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">out2=<file> (outnonmatch2) Use this to write 2nd read of pairs to a</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.IP</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">different file.</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.PP</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">outm=<file> (outmatch) Write reads here that fail filters. In default</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.TP</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">kfilter mode, this means any read with a matching kmer.</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">In any mode, it also includes reads that fail filters such</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">as minlength, mingc, maxgc, entropy, etc. In other words,</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">it includes all reads that do not go to 'out'.</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.PP</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">outm2=<file> (outmatch2) Use this to write 2nd read of pairs to a</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.IP</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">different file.</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.PP</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">outs=<file> (outsingle) Use this to write singleton reads whose mate</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.IP</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">was trimmed shorter than minlen.</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.PP</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">stats=<file> Write statistics about which contamininants were detected.</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">refstats=<file> Write statistics on a per\-reference\-file basis.</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">rpkm=<file> Write RPKM for each reference sequence (for RNA\-seq).</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">dump=<file> Dump kmer tables to a file, in fasta format.</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">duk=<file> Write statistics in duk's format. *DEPRECATED*</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">nzo=t Only write statistics about ref sequences with nonzero hits.</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">overwrite=t (ow) Grant permission to overwrite files.</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">showspeed=t (ss) 'f' suppresses display of processing speed.</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">ziplevel=2 (zl) Compression level; 1 (min) through 9 (max).</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">fastawrap=70 Length of lines in fasta output.</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">qout=auto Output quality offset: 33 (Sanger), 64, or auto.</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">statscolumns=3 (cols) Number of columns for stats output, 3 or 5.</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">.IP</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">5 includes base counts.</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">.PP</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">rename=f Rename reads to indicate which sequences they matched.</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">refnames=f Use names of reference files rather than scaffold IDs.</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">trd=f Truncate read and ref names at the first whitespace.</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">ordered=f Set to true to output reads in same order as input.</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">maxbasesout=\-1 If positive, quit after writing approximately this many</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">.IP</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">bases to out (outu/outnonmatch).</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">.PP</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">maxbasesoutm=\-1 If positive, quit after writing approximately this many</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">.IP</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">bases to outm (outmatch).</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">.PP</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">json=f Print to screen in json format.</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">.PP</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">Histogram output parameters:</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">bhist=<file> Base composition histogram by position.</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">qhist=<file> Quality histogram by position.</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">qchist=<file> Count of bases with each quality value.</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">aqhist=<file> Histogram of average read quality.</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">bqhist=<file> Quality histogram designed for box plots.</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">lhist=<file> Read length histogram.</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">phist=<file> Polymer length histogram.</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">gchist=<file> Read GC content histogram.</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">ihist=<file> Insert size histogram, for paired reads in mapped sam.</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">gcbins=100 Number gchist bins. Set to 'auto' to use read length.</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">maxhistlen=6000 Set an upper bound for histogram lengths; higher uses</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">.TP</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">more memory.</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">The default is 6000 for some histograms</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">.IP</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">and 80000 for others.</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">.PP</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">Histograms for mapped sam/bam files only:</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">histbefore=t Calculate histograms from reads before processing.</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">ehist=<file> Errors\-per\-read histogram.</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">qahist=<file> Quality accuracy histogram of error rates versus quality</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">.IP</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">score.</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">.PP</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">indelhist=<file> Indel length histogram.</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">mhist=<file> Histogram of match, sub, del, and ins rates by position.</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">idhist=<file> Histogram of read count versus percent identity.</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">idbins=100 Number idhist bins. Set to 'auto' to use read length.</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">varfile=<file> Ignore substitution errors listed in this file when</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">.TP</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">calculating error rates.</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">Can be generated with</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">.IP</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">CallVariants.</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">.PP</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">vcf=<file> Ignore substitution errors listed in this VCF file</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">.IP</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">when calculating error rates.</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">.PP</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">ignorevcfindels=t Also ignore indels listed in the VCF.</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">.PP</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">Processing parameters:</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">k=27 Kmer length used for finding contaminants. Contaminants</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">.TP</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">shorter than k will not be found.</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">k must be at least 1.</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">.PP</span>
</pre>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">rcomp=t Look for reverse\-complements of kmers in addition to</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">.IP</span>
</pre>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">forward kmers.</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">.PP</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">.IP</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">increase sensitivity in the presence of errors.</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">.PP</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">minkmerhits=1 (mkh) Reads need at least this many matching kmers</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">.IP</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">to be considered as matching the reference.</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">.PP</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">.TP</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">kmers to hit a ref, in order to be considered a match.</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">If this and minkmerhits are set, the greater is used.</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">.PP</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">.TP</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">bases to be covered by ref kmers to be considered a match.</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">If specified, mcf overrides mkh and mkf.</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">.PP</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only).</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">.IP</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">Memory use is proportional to (3*K)^hdist.</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">.PP</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">qhdist=0 Hamming distance for query kmers; impacts speed, not memory.</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">editdistance=0 (edist) Maximum edit distance from ref kmers (subs</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">.TP</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">and indels).</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">Memory use is proportional to (8*K)^edist.</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">.PP</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink.</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">qhdist2=0 Sets qhdist for short kmers, when using mink.</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">editdistance2=0 (edist2) Sets edist for short kmers, when using mink.</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">forbidn=f (fn) Forbids matching of read kmers containing N.</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">.TP</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">By default, these will match a reference 'A' if</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">hdist>0 or edist>0, to increase sensitivity.</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">.PP</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">.TP</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">match (or either is trimmed shorter than minlen).</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">Set to false to require both.</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">.PP</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">trimfailures=f Instead of discarding failed reads, trim them to 1bp.</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">.IP</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">This makes the statistics a bit odd.</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">.PP</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">findbestmatch=f (fbm) If multiple matches, associate read with sequence</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">.TP</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">sharing most kmers.</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">Reduces speed.</span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">.PP</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">skipr1=f Don't do kmer\-based operations on read 1.</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">skipr2=f Don't do kmer\-based operations on read 2.</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">ecco=f For overlapping paired reads only. Performs errorcorrection with BBMerge prior to kmer operations.</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">recalibrate=f (recal) Recalibrate quality scores. Requires calibration</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">.IP</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">matrices generated by CalcTrueQuality.</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">.PP</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">sam=<file,file> If recalibration is desired, and matrices have not already</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">.IP</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">been generated, BBDuk will create them from the sam file.</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">.PP</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">amino=f Run in amino acid mode. Some features have not been</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">tested, but kmer\-matching works fine.</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">Maximum k is 12.</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">Speed and Memory parameters:</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">threads=auto (t) Set number of threads to use; default is number of</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">logical processors.</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">prealloc=f Preallocate memory in table. Allows faster table loading</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">and more efficient memory usage, for a large reference.</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">.PP</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">monitor=f Kill this process if it crashes. monitor=600,0.01 would</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">.IP</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">kill after 600 seconds under 1% usage.</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">.PP</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">minrskip=1 (mns) Force minimal skip interval when indexing reference</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">.TP</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">kmers.</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">1 means use all, 2 means use every other kmer, etc.</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">.PP</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">maxrskip=1 (mxs) Restrict maximal skip interval when indexing</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">.TP</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">reference kmers. Normally all are used for scaffolds<100kb,</span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">but with longer scaffolds, up to maxrskip\-1 are skipped.</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">.PP</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">rskip= Set both minrskip and maxrskip to the same value.</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">.IP</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">If not set, rskip will vary based on sequence length.</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">.PP</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">qskip=1 Skip query kmers to increase speed. 1 means use all.</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">speed=0 Ignore this fraction of kmer space (0\-15 out of 16) in both</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">.TP</span>
</pre>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">reads and reference.</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">Increases speed and reduces memory.</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">.PP</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">Note: Do not use more than one of 'speed', 'qskip', and 'rskip'.</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">.PP</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">Trimming/Filtering/Masking parameters:</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">Note \- if ktrim, kmask, and ksplit are unset, the default behavior is kfilter.</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">All kmer processing modes are mutually exclusive.</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">Reads only get sent to 'outm' purely based on kmer matches in kfilter mode.</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">.PP</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">ktrim=f Trim reads to remove bases matching reference kmers.</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">.TP</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">Values:</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">f (don't trim),</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">r (trim to the right),</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">l (trim to the left)</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">.PP</span>
</pre>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">kmask= Replace bases matching ref kmers with another symbol.</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">.TP</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext">Allows any non\-whitespace character, and processes short</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">kmers on both ends if mink is set. 'kmask=lc' will</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">convert masked bases to lowercase.</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">.PP</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers.</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">ksplit=f For single\-ended reads only. Reads will be split into</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">.TP</span>
</pre>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">pairs around the kmer.</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">If the kmer is at the end of the</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">.TP</span>
</pre>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">read, it will be trimmed instead.</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">Singletons will go to</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">.TP</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">out, and pairs will go to outm.</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">Do not use ksplit with</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">other operations such as quality\-trimming or filtering.</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">.PP</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">mink=0 Look for shorter kmers at read tips down to this length,</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">.TP</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">when k\-trimming or masking.</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">0 means disabled. Enabling</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">.IP</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">this will disable maskmiddle.</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">.PP</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">qtrim=f Trim read ends to remove bases with quality below trimq.</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">.TP</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">Performed AFTER looking for kmers.</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">Values:</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">.TP</span>
</pre>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">rl (trim both ends),</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">f (neither end),</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">r (right end only),</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">l (left end only),</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">w (sliding window).</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">.PP</span>
</pre>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">trimq=6 Regions with average quality BELOW this will be trimmed,</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">.TP</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">if qtrim is set to something other than f.</span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">Can be a</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">.IP</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">floating\-point number like 7.3.</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">.PP</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">trimclip=f Trim soft\-clipped bases from sam files.</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">minlength=10 (ml) Reads shorter than this after trimming will be</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">.TP</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">discarded.</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">Pairs will be discarded if both are shorter.</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext">.PP</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext">mlf=0 (minlengthfraction) Reads shorter than this fraction of</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">.IP</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">original length after trimming will be discarded.</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">.PP</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">maxlength= Reads longer than this after trimming will be discarded.</span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">.IP</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">Pairs will be discarded only if both are longer.</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">.PP</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">minavgquality=0 (maq) Reads with average quality (after trimming) below</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">.IP</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">this will be discarded.</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">.PP</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">maqb=0 If positive, calculate maq from this many initial bases.</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">minbasequality=0 (mbq) Reads with any base below this quality (after</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext">trimming) will be discarded.</span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext">maxns=\-1 If non\-negative, reads with more Ns than this</span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">(after trimming) will be discarded.</span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext">mcb=0 (minconsecutivebases) Discard reads without at least</span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext">this many consecutive called bases.</span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext">than minlength to outm rather than discarding.</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext">tp=0 (trimpad) Trim this much extra around matching kmers.</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">tbo=f (trimbyoverlap) Trim adapters based on where paired</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext">reads overlap.</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext">strictoverlap=t Adjust sensitivity for trimbyoverlap mode.</span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext">minoverlap=14 Require this many bases of overlap for detection.</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext">mininsert=40 Require insert size of at least this for overlap.</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">Should be reduced to 16 for small RNA sequencing.</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext">.PP</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">tpe=f (trimpairsevenly) When kmer right\-trimming, trim both</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext">.IP</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext">reads to the minimum length of either.</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext">.PP</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext">forcetrimleft=0 (ftl) If positive, trim bases to the left of this position</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext">.IP</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext">(exclusive, 0\-based).</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext">.PP</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext">forcetrimright=0 (ftr) If positive, trim bases to the right of this position</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext">.IP</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">(exclusive, 0\-based).</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext">.PP</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext">forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end.</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext">forcetrimmod=0 (ftm) If positive, right\-trim length to be equal to zero,</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext">.IP</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext">modulo this number.</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext">.PP</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext">restrictleft=0 If positive, only look for kmer matches in the</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext">.IP</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext">leftmost X bases.</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext">.PP</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext">restrictright=0 If positive, only look for kmer matches in the</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext">.IP</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext">rightmost X bases.</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext">.PP</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext">mingc=0 Discard reads with GC content below this.</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext">maxgc=1 Discard reads with GC content above this.</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext">gcpairs=t Use average GC of paired reads.</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext">.IP</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext">Also affects gchist.</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext">.PP</span>
</pre>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext">tossjunk=f Discard reads with invalid characters as bases.</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext">swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2.</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext">.PP</span>
</pre>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext">Header\-parsing parameters \- these require Illumina headers:</span>
</pre>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext">chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'.</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext">barcodefilter=f Remove reads with unexpected barcodes if barcodes is set,</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext">.TP</span>
</pre>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext">or barcodes containing 'N' otherwise.</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext">A barcode must be</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext">.TP</span>
</pre>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext">the last part of the read header.</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext">Values:</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext">.TP</span>
</pre>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext">t:</span>
</pre>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext">Remove reads with bad barcodes.</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext">.TP</span>
</pre>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext">f:</span>
</pre>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="plaintext">Ignore barcodes.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="plaintext">.IP</span>
</pre>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="plaintext">crash: Crash upon encountering bad barcodes.</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="plaintext">.PP</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="plaintext">barcodes= Comma\-delimited list of barcodes or files of barcodes.</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="plaintext">xmin=\-1 If positive, discard reads with a lesser X coordinate.</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext">ymin=\-1 If positive, discard reads with a lesser Y coordinate.</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext">xmax=\-1 If positive, discard reads with a greater X coordinate.</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext">ymax=\-1 If positive, discard reads with a greater Y coordinate.</span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext">.PP</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext">Polymer trimming:</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext">trimpolya=0 If greater than 0, trim poly\-A or poly\-T tails of</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext">.IP</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext">at least this length on either end of reads.</span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext">.PP</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="plaintext">trimpolygleft=0 If greater than 0, trim poly\-G prefixes of at least this</span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="plaintext">.TP</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext">length on the left end of reads.</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="plaintext">Does not trim poly\-C.</span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="plaintext">.PP</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext">trimpolygright=0 If greater than 0, trim poly\-G tails of at least this</span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext">.TP</span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="plaintext">length on the right end of reads.</span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="plaintext">Does not trim poly\-C.</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="plaintext">.PP</span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="plaintext">trimpolyg=0 This sets both left and right at once.</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="plaintext">filterpolyg=0 If greater than 0, remove reads with a poly\-G prefix of</span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="plaintext">.IP</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="plaintext">at least this length (on the left).</span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="plaintext">.PP</span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="plaintext">Note: there are also equivalent poly\-C flags.</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="plaintext">.PP</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="plaintext">Polymer tracking:</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext">pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers.</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="plaintext">plen=20 Length of homopolymers to count.</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="plaintext">.PP</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext">Entropy/Complexity parameters:</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="plaintext">entropy=\-1 Set between 0 and 1 to filter reads with entropy below</span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="plaintext">.TP</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="plaintext">that value.</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext">Higher is more stringent.</span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext">.PP</span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext">entropywindow=50 Calculate entropy using a sliding window of this length.</span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext">entropyk=5 Calculate entropy using kmers of this length.</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext">minbasefrequency=0 Discard reads with a minimum base frequency below this.</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext">entropymask=f Values:</span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="plaintext">.TP</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext">f:</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="plaintext">Discard low\-entropy sequences.</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="plaintext">.TP</span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext">t:</span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext">Mask low\-entropy parts of sequences with N.</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="plaintext">.IP</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext">lc: Change low\-entropy parts of sequences to lowercase.</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext">.PP</span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="plaintext">entropymark=f Mark each base with its entropy value. This is on a scale</span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="plaintext">.TP</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="plaintext">of 0\-41 and is reported as quality scores, so the output</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="plaintext">should be fastq or fasta+qual.</span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="plaintext">.PP</span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="plaintext">Cardinality estimation:</span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext">cardinality=f (loglog) Count unique kmers using the LogLog algorithm.</span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="plaintext">cardinalityout=f (loglogout) Count unique kmers in output reads.</span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="plaintext">loglogk=31 Use this kmer length for counting.</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="plaintext">loglogbuckets=1999 Use this many buckets for counting.</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="plaintext">.PP</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext">Java Parameters:</span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="plaintext">.PP</span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="plaintext">\fB\-Xmx\fR This will set Java's memory usage, overriding autodetection.</span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext">.TP</span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext">\fB\-Xmx20g\fR will</span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext">specify 20 gigs of RAM, and \fB\-Xmx200m\fR will specify 200 megs.</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext">The max is typically 85% of physical memory.</span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext">.PP</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext">\fB\-eoom\fR This flag will cause the process to exit if an</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext">.TP</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext">out\-of\-memory exception occurs.</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext">Requires Java 8u92+.</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext">.PP</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext">\fB\-da\fR Disable assertions.</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext">.PP</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext">Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext">.SH AUTHOR</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/bbmap/commit/3758d4c612caa1e1f97bf4d89e5ef85f1f08d4e2#e48989d0b76f7deb176080cdbf75bd638e725fac"><strong>debian/bbmap.sh.1</strong>
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<strong>debian/mans/bbmap.sh.1</strong>
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<a href="https://salsa.debian.org/med-team/bbmap/commit/3758d4c612caa1e1f97bf4d89e5ef85f1f08d4e2#776b4112df8d10cf7cb1347f0dd6fffea9a7f193"><strong>debian/mans/bbnorm.sh.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BBNORM.SH "1" "April 2019" "bbnorm.sh 38.43" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">bbnorm.sh \- Kmer-based error-correction and normalization tool</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B bbnorm.sh</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,in=<input> out=<reads to keep> outt=<reads to toss> hist=<histogram output>\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Written by Brian Bushnell</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Last modified October 19, 2017</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Description: Normalizes read depth based on kmer counts.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Can also error\-correct, bin reads by kmer depth, and generate a kmer depth histogram.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">However, Tadpole has superior error\-correction to BBNorm.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Please read bbmap/docs/guides/BBNormGuide.txt for more information.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Input parameters:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">in=null Primary input. Use in2 for paired reads in a second file</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">in2=null Second input file for paired reads in two files</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">extra=null Additional files to use for input (generating hash table) but not for output</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">tablereads=\-1 Use at most this many reads when building the hashtable (\fB\-1\fR means all)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">kmersample=1 Process every nth kmer, and skip the rest</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">readsample=1 Process every nth read, and skip the rest</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">interleaved=auto May be set to true or false to force the input read file to ovverride autodetection of the input file as paired interleaved.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Output parameters:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">out=<file> File for normalized or corrected reads. Use out2 for paired reads in a second file</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">outt=<file> (outtoss) File for reads that were excluded from primary output</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">reads=\-1 Only process this number of reads, then quit (\fB\-1\fR means all)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1)</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">keepall=f Set to true to keep all reads (e.g. if you just want error correction).</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">zerobin=f Set to true if you want kmers with a count of 0 to go in the 0 bin instead of the 1 bin in histograms.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Default is false, to prevent confusion about how there can be 0\-count kmers.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">rename=f Rename reads based on their kmer depth.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Hashing parameters:</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported)</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">bits=32 Bits per cell in bloom filter; must be 2, 4, 8, 16, or 32. Maximum kmer depth recorded is 2^cbits. Automatically reduced to 16 in 2\-pass.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest\-depth kmers.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">hashes=3 Number of times each kmer is hashed and stored. Higher is slower.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">prefilter=f True is slower, but generally more accurate; filters out low\-depth kmers from the main hashtable. The prefilter is more memory\-efficient because it uses 2\-bit cells.</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">prehashes=2 Number of hashes for prefilter.</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">prefilterbits=2 (pbits) Bits per cell in prefilter.</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">prefiltersize=0.35 Fraction of memory to allocate to prefilter.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low\-depth kmers</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">minq=6 Ignore kmers containing bases with quality below this</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">minprob=0.5 Ignore kmers with overall probability of correctness below this</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">threads=auto (t) Spawn exactly X hashing threads (default is number of logical processors). Total active threads may exceed X due to I/O threads.</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">rdk=t (removeduplicatekmers) When true, a kmer's count will only be incremented once per read pair, even if that kmer occurs more than once.</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">Normalization parameters:</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">fixspikes=f (fs) Do a slower, high\-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions.</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth.</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">For kmer depth Dk, read depth Dr, read length R, and kmer size K:</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">Dr=Dk*(R/(R\-K+1))</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">maxdepth=\-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth.</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read.</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'.</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">percentile=54.0 (dp) Read depth is by default inferred from the 54th percentile of kmer depth, but this may be changed to any number 1\-100.</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy.</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads.</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth.</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">Error detection parameters:</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth.</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth.</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">tossbadreads=f (tbr) Throw away reads detected as containing errors.</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">requirebothbad=f (rbb) Only toss bad pairs if both reads are bad.</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">errordetectratio=125 (edr) Reads with a ratio of at least this much between their high and low depth kmers will be classified as error reads.</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non\-error.</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors.</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">Error correction parameters:</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job.</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged.</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error.</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non\-error.</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors.</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">eccmaxqual=127 Do not correct bases with quality above this value.</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3.</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4.</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything.</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'.</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">overlap=f (ecco) Error correct by read overlap.</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">Depth binning parameters:</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">lowbindepth=10 (lbd) Cutoff for low depth bin.</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">highbindepth=80 (hbd) Cutoff for high depth bin.</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">outlow=<file> Pairs in which both reads have a median below lbd go into this file.</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">outhigh=<file> Pairs in which both reads have a median above hbd go into this file.</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">outmid=<file> All other pairs go into this file.</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">Histogram parameters:</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">hist=<file> Specify a file to write the input kmer depth histogram.</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">histout=<file> Specify a file to write the output kmer depth histogram.</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3.</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">pzc=f (printzerocoverage) Print lines in the histogram with zero coverage.</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization.</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">Peak calling parameters:</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">peaks=<file> Write the peaks to this file. Default is stdout.</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">minHeight=2 (h) Ignore peaks shorter than this.</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">minVolume=5 (v) Ignore peaks with less area than this.</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">minWidth=3 (w) Ignore peaks narrower than this.</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">minPeak=2 (minp) Ignore peaks with an X\-value below this.</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">maxPeak=BIG (maxp) Ignore peaks with an X\-value above this.</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height).</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">.PP</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">Java Parameters:</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">\fB\-Xmx\fR This will set Java's memory usage, overriding autodetection.</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">.TP</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">\fB\-Xmx20g\fR will specify 20 gigs of RAM, and \fB\-Xmx200m\fR will specify 200 megs.</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">The max is typically 85% of physical memory.</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">.PP</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">\fB\-eoom\fR This flag will cause the process to exit if an</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">.TP</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">out\-of\-memory exception occurs.</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">Requires Java 8u92+.</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">.PP</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">\fB\-da\fR Disable assertions.</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">.PP</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">.SH AUTHOR</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/bbmap/commit/3758d4c612caa1e1f97bf4d89e5ef85f1f08d4e2#c29173014674b2df3174c8a8fd476346903b30fb"><strong>debian/bloomfilter.sh.1</strong>
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<strong>debian/mans/bloomfilter.sh.1</strong>
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<a href="https://salsa.debian.org/med-team/bbmap/commit/3758d4c612caa1e1f97bf4d89e5ef85f1f08d4e2#d864ddf62aef569bfeed5f2b1577c945be7a286c"><strong>debian/mans/dedupe.sh.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH DEDUPE.SH "1" "April 2019" "dedupe.sh 38.43" "User Commands"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">dedupe.sh \- Simplifies assemblies by removing duplicate or contained</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B dedupe.sh</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,in=<file or stdin> out=<file or stdout>\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Written by Brian Bushnell and Jonathan Rood</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Last modified November 20, 2017</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Description: Accepts one or more files containing sets of sequences (reads or scaffolds).</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Removes duplicate sequences, which may be specified to be exact matches, subsequences, or sequences within some percent identity.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Can also find overlapping sequences and group them into clusters.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Please read bbmap/docs/guides/DedupeGuide.txt for more information.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">An example of running Dedupe for clustering short reads:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">dedupe.sh in=x.fq am=f ac=f fo c pc rnc=f mcs=4 mo=100 s=1 pto cc qin=33 csf=stats.txt pattern=cluster_%.fq dot=graph.dot</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Input may be fasta or fastq, compressed or uncompressed.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Output may be stdout or a file. With no output parameter, data will be written to stdout.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">If 'out=null', there will be no output, but statistics will still be printed.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">You can also use 'dedupe <infile> <outfile>' without the 'in=' and 'out='.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">I/O parameters:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">in=<file,file> A single file or a comma\-delimited list of files.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">out=<file> Destination for all output contigs.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">pattern=<file> Clusters will be written to individual files, where the '%' symbol in the pattern is replaced by cluster number.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">outd=<file> Optional; removed duplicates will go here.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">csf=<file> (clusterstatsfile) Write a list of cluster names and sizes.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">dot=<file> (graph) Write a graph in dot format. Requires 'fo' and 'pc' flags.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">threads=auto (t) Set number of threads to use; default is number of logical processors.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">overwrite=t (ow) Set to false to force the program to abort rather than overwrite an existing file.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">showspeed=t (ss) Set to 'f' to suppress display of processing speed.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">minscaf=0 (ms) Ignore contigs/scaffolds shorter than this.</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">interleaved=auto If true, forces fastq input to be paired and interleaved.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">ziplevel=2 Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Output format parameters:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">storename=t (sn) Store scaffold names (set false to save memory).</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">#addpairnum=f Add .1 and .2 to numeric id of read1 and read2.</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">storequality=t (sq) Store quality values for fastq assemblies (set false to save memory).</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">uniquenames=t (un) Ensure all output scaffolds have unique names. Uses more memory.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">numbergraphnodes=t (ngn) Label dot graph nodes with read numbers rather than read names.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">sort=f Sort output (otherwise it will be random). Options:</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">length:</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Sort by length</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">quality: Sort by quality</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">name: Sort by name</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">id: Sort by input order</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">ascending=f Sort in ascending order.</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">ordered=f Output sequences in input order. Equivalent to sort=id ascending.</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">renameclusters=f (rnc) Rename contigs to indicate which cluster they are in.</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">printlengthinedges=f (ple) Print the length of contigs in edges.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">Processing parameters:</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">absorbrc=t (arc) Absorb reverse\-complements as well as normal orientation.</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">absorbmatch=t (am) Absorb exact matches of contigs.</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">absorbcontainment=t (ac) Absorb full containments of contigs.</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">#absorboverlap=f (ao) Absorb (merge) non\-contained overlaps of contigs (TODO).</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">findoverlap=f (fo) Find overlaps between contigs (containments and non\-containments). Necessary for clustering.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">uniqueonly=f (uo) If true, all copies of duplicate reads will be discarded, rather than keeping 1.</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">rmn=f (requirematchingnames) If true, both names and sequence must match.</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">usejni=f (jni) Do alignments in C code, which is faster, if an edit distance is allowed.</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">This will require compiling the C code; details are in \fI\,/jni/README.txt\/\fP.</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">Subset parameters:</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">subsetcount=1 (sstc) Number of subsets used to process the data; higher uses less memory.</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">subset=0 (sst) Only process reads whose ((ID%subsetcount)==subset).</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">Clustering parameters:</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">cluster=f (c) Group overlapping contigs into clusters.</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">pto=f (preventtransitiveoverlaps) Do not look for new edges between nodes in the same cluster.</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">minclustersize=1 (mcs) Do not output clusters smaller than this.</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">pbr=f (pickbestrepresentative) Only output the single highest\-quality read per cluster.</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">.PP</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">Cluster postprocessing parameters:</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">processclusters=f (pc) Run the cluster processing phase, which performs the selected operations in this category.</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">.IP</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">For example, pc AND cc must be enabled to perform cc.</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.PP</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">fixmultijoins=t (fmj) Remove redundant overlaps between the same two contigs.</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">removecycles=t (rc) Remove all cycles so clusters form trees.</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">cc=t (canonicizeclusters) Flip contigs so clusters have a single orientation.</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">fcc=f (fixcanoncontradictions) Truncate graph at nodes with canonization disputes.</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">foc=f (fixoffsetcontradictions) Truncate graph at nodes with offset disputes.</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">mst=f (maxspanningtree) Remove cyclic edges, leaving only the longest edges that form a tree.</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">.PP</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">Overlap Detection Parameters</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">exact=t (ex) Only allow exact symbol matches. When false, an 'N' will match any symbol.</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">touppercase=t (tuc) Convert input bases to upper\-case; otherwise, lower\-case will not match.</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">maxsubs=0 (s) Allow up to this many mismatches (substitutions only, no indels). May be set higher than maxedits.</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">maxedits=0 (e) Allow up to this many edits (subs or indels). Higher is slower.</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">minidentity=100 (mid) Absorb contained sequences with percent identity of at least this (includes indels).</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">minlengthpercent=0 (mlp) Smaller contig must be at least this percent of larger contig's length to be absorbed.</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">minoverlappercent=0 (mop) Overlap must be at least this percent of smaller contig's length to cluster and merge.</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">minoverlap=200 (mo) Overlap must be at least this long to cluster and merge.</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">depthratio=0 (dr) When non\-zero, overlaps will only be formed between reads with a depth ratio of at most this.</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.TP</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">Should be above 1.</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">Depth is determined by parsing the read names; this information can be added</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.IP</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">by running KmerNormalize (khist.sh, bbnorm.sh, or ecc.sh) with the flag 'rename'</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">.PP</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">k=31 Seed length used for finding containments and overlaps. Anything shorter than k will not be found.</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">numaffixmaps=1 (nam) Number of prefixes/suffixes to index per contig. Higher is more sensitive, if edits are allowed.</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">hashns=f Set to true to search for matches using kmers containing Ns. Can lead to extreme slowdown in some cases.</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">#ignoreaffix1=f (ia1) Ignore first affix (for testing).</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">#storesuffix=f (ss) Store suffix as well as prefix. Automatically set to true when doing inexact matches.</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">.PP</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">Other Parameters</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">qtrim=f Set to qtrim=rl to trim leading and trailing Ns.</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">trimq=6 Quality trim level.</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">forcetrimleft=\-1 (ftl) If positive, trim bases to the left of this position (exclusive, 0\-based).</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">forcetrimright=\-1 (ftr) If positive, trim bases to the right of this position (exclusive, 0\-based).</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">.PP</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">Note on Proteins / Amino Acids</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">Dedupe supports amino acid space via the 'amino' flag. This also changes the default kmer length to 10.</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">In amino acid mode, all flags related to canonicity and reverse\-complementation are disabled,</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">and nam (numaffixmaps) is currently limited to 2 per tip.</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">.PP</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">Java Parameters:</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">\fB\-Xmx\fR This will set Java's memory usage, overriding autodetection.</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">.TP</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">\fB\-Xmx20g\fR will specify 20 gigs of RAM, and \fB\-Xmx200m\fR will specify 200 megs.</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">The max is typically 85% of physical memory.</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">.PP</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">\fB\-eoom\fR This flag will cause the process to exit if an out\-of\-memory exception occurs. Requires Java 8u92+.</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">\fB\-da\fR Disable assertions.</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">.PP</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">.SH AUTHOR</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="b6d717b880589b8f373a3fcb153c36a91c5f439e">
<a href="https://salsa.debian.org/med-team/bbmap/commit/3758d4c612caa1e1f97bf4d89e5ef85f1f08d4e2#b6d717b880589b8f373a3fcb153c36a91c5f439e"><strong>debian/mans/reformat.sh.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH REFORMAT.SH "1" "April 2019" "reformat.sh 38.43" "User Commands"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">reformat.sh \- Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B reformat.sh</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,in=<file> in2=<file2> out=<outfile> out2=<outfile2>\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Written by Brian Bushnell</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Last modified February 21, 2019</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.PP</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Description: Reformats reads to change ASCII quality encoding, interleaving, file format, or compression format.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Optionally performs additional functions such as quality trimming, subsetting, and subsampling.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Supports fastq, fasta, fasta+qual, scarf, oneline, sam, bam, gzip, bz2.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Please read bbmap/docs/guides/ReformatGuide.txt for more information.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">in2 and out2 are for paired reads and are optional.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">If input is paired and there is only one output file, it will be written interleaved.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Parameters and their defaults:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">ow=f (overwrite) Overwrites files that already exist.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">app=f (append) Append to files that already exist.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">int=f (interleaved) Determines whether INPUT file is considered interleaved.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">fastawrap=70 Length of lines in fasta output.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">fastareadlen=0 Set to a non\-zero number to break fasta files into reads of at most this length.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">fastaminlen=1 Ignore fasta reads shorter than this.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">qfake=30 Quality value used for fasta to fastq reformatting.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">qfin=<.qual file> Read qualities from this qual file, for the reads coming from 'in=<fasta file>'</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">qfin2=<.qual file> Read qualities from this qual file, for the reads coming from 'in2=<fasta file>'</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">qfout=<.qual file> Write qualities from this qual file, for the reads going to 'out=<fasta file>'</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">qfout2=<.qual file> Write qualities from this qual file, for the reads coming from 'out2=<fasta file>'</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">outsingle=<file> (outs) If a read is longer than minlength and its mate is shorter, the longer one goes here.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">deleteinput=f Delete input upon successful completion.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">ref=<file> Optional reference fasta for sam processing.</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Processing Parameters:</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">verifypaired=f (vpair) When true, checks reads to see if the names look paired. Prints an error message if not.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">verifyinterleaved=f (vint) sets 'vpair' to true and 'interleaved' to true.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">allowidenticalnames=f (ain) When verifying pair names, allows identical names, instead of requiring \fI\,/1\/\fP and \fI\,/2\/\fP or 1: and 2:</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">tossbrokenreads=f (tbr) Discard reads that have different numbers of bases and qualities. By default this will be detected and cause a crash.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">ignorebadquality=f (ibq) Fix out\-of\-range quality values instead of crashing with a warning.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">addslash=f Append ' /1' and ' /2' to read names, if not already present. Please include the flag 'int=t' if the reads are interleaved.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">spaceslash=t Put a space before the slash in addslash mode.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">addcolon=f Append ' 1:' and ' 2:' to read names, if not already present. Please include the flag 'int=t' if the reads are interleaved.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">underscore=f Change whitespace in read names to underscores.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">rcomp=f (rc) Reverse\-compliment reads.</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">rcompmate=f (rcm) Reverse\-compliment read 2 only.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">changequality=t (cq) N bases always get a quality of 0 and ACGT bases get a min quality of 2.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">quantize=f Quantize qualities to a subset of values like NextSeq. Can also be used with comma\-delimited list, like quantize=0,8,13,22,27,32,37</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">tuc=f (touppercase) Change lowercase letters in reads to uppercase.</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">uniquenames=f Make duplicate names unique by appending _<number>.</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">remap= A set of pairs: remap=CTGN will transform C>T and G>N.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">Use remap1 and remap2 to specify read 1 or 2.</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">iupacToN=f (itn) Convert non\-ACGTN symbols to N.</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">monitor=f Kill this process if it crashes. monitor=600,0.01 would kill after 600 seconds under 1% usage.</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">crashjunk=t Crash when encountering reads with invalid bases.</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">tossjunk=f Discard reads with invalid characters as bases.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">fixjunk=f Convert invalid bases to N.</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">fixheaders=f Convert nonstandard header characters to standard ASCII.</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">recalibrate=f (recal) Recalibrate quality scores. Must first generate matrices with CalcTrueQuality.</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">maxcalledquality=41 Quality scores capped at this upper bound.</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">mincalledquality=2 Quality scores of ACGT bases will be capped at lower bound.</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">trimreaddescription=f (trd) Trim the names of reads after the first whitespace.</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">trimrname=f For sam/bam files, trim rname/rnext fields after the first space.</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">fixheaders=f Replace characters in headers such as space, *, and | to make them valid file names.</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">warnifnosequence=t For fasta, issue a warning if a sequenceless header is encountered.</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">warnfirsttimeonly=t Issue a warning for only the first sequenceless header.</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">utot=f Convert U to T (for RNA \-> DNA translation).</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">padleft=0 Pad the left end of sequences with this many symbols.</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">padright=0 Pad the right end of sequences with this many symbols.</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">pad=0 Set padleft and padright to the same value.</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">padsymbol=N Symbol to use for padding.</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">.PP</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">Histogram output parameters:</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">.PP</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">bhist=<file> Base composition histogram by position.</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">qhist=<file> Quality histogram by position.</span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">qchist=<file> Count of bases with each quality value.</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">aqhist=<file> Histogram of average read quality.</span>
</pre>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">bqhist=<file> Quality histogram designed for box plots.</span>
</pre>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">lhist=<file> Read length histogram.</span>
</pre>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">gchist=<file> Read GC content histogram.</span>
</pre>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">gcbins=100 Number gchist bins. Set to 'auto' to use read length.</span>
</pre>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">gcplot=f Add a graphical representation to the gchist.</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">maxhistlen=6000 Set an upper bound for histogram lengths; higher uses more memory.</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">.IP</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">The default is 6000 for some histograms and 80000 for others.</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">.PP</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">Histograms for sam files only (requires sam format 1.4 or higher):</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">.PP</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">ehist=<file> Errors\-per\-read histogram.</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">qahist=<file> Quality accuracy histogram of error rates versus quality score.</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">indelhist=<file> Indel length histogram.</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">mhist=<file> Histogram of match, sub, del, and ins rates by read location.</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">ihist=<file> Insert size histograms. Requires paired reads in a sam file.</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">idhist=<file> Histogram of read count versus percent identity.</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">idbins=100 Number idhist bins. Set to 'auto' to use read length.</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">.PP</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">Sampling parameters:</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">.PP</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">reads=\-1 Set to a positive number to only process this many INPUT reads (or pairs), then quit.</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">skipreads=\-1 Skip (discard) this many INPUT reads before processing the rest.</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">samplerate=1 Randomly output only this fraction of reads; 1 means sampling is disabled.</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">sampleseed=\-1 Set to a positive number to use that prng seed for sampling (allowing deterministic sampling).</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">samplereadstarget=0 (srt) Exact number of OUTPUT reads (or pairs) desired.</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">samplebasestarget=0 (sbt) Exact number of OUTPUT bases desired.</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">.IP</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">Important: srt/sbt flags should not be used with stdin, samplerate, qtrim, minlength, or minavgquality.</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">.PP</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">upsample=f Allow srt/sbt to upsample (duplicate reads) when the target is greater than input.</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">prioritizelength=f If true, calculate a length threshold to reach the target, and retain all reads of at least that length (must set srt or sbt).</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">.PP</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">Trimming and filtering parameters:</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">.PP</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">qtrim=f Trim read ends to remove bases with quality below trimq.</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">.IP</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">Values: t (trim both ends), f (neither end), r (right end only), l (left end only), w (sliding window).</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">.PP</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">trimq=6 Regions with average quality BELOW this will be trimmed. Can be a floating\-point number like 7.3.</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">minlength=0 (ml) Reads shorter than this after trimming will be discarded. Pairs will be discarded only if both are shorter.</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">mlf=0 (mlf) Reads shorter than this fraction of original length after trimming will be discarded.</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">maxlength=0 If nonzero, reads longer than this after trimming will be discarded.</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">breaklength=0 If nonzero, reads longer than this will be broken into multiple reads of this length. Does not work for paired reads.</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">requirebothbad=t (rbb) Only discard pairs if both reads are shorter than minlen.</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">invertfilters=f (invert) Output failing reads instead of passing reads.</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">minavgquality=0 (maq) Reads with average quality (after trimming) below this will be discarded.</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">maqb=0 If positive, calculate maq from this many initial bases.</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">chastityfilter=f (cf) Reads with names containing ' 1:Y:' or ' 2:Y:' will be discarded.</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, or barcodes containing 'N' otherwise.</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">.IP</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">A barcode must be the last part of the read header.</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">.PP</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">barcodes= Comma\-delimited list of barcodes or files of barcodes.</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">maxns=\-1 If 0 or greater, reads with more Ns than this (after trimming) will be discarded.</span>
</pre>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">minconsecutivebases=0 (mcb) Discard reads without at least this many consecutive called bases.</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">forcetrimleft=0 (ftl) If nonzero, trim left bases of the read to this position (exclusive, 0\-based).</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">forcetrimright=0 (ftr) If nonzero, trim right bases of the read after this position (exclusive, 0\-based).</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end.</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">forcetrimmod=5 (ftm) If positive, trim length to be equal to zero modulo this number.</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">mingc=0 Discard reads with GC content below this.</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">maxgc=1 Discard reads with GC content above this.</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">gcpairs=t Use average GC of paired reads.</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">.IP</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">Also affects gchist.</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">.PP</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">Sam and bam processing options:</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">.PP</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">mappedonly=f Toss unmapped reads.</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">unmappedonly=f Toss mapped reads.</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">pairedonly=f Toss reads that are not mapped as proper pairs.</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">unpairedonly=f Toss reads that are mapped as proper pairs.</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">primaryonly=f Toss secondary alignments. Set this to true for sam to fastq conversion.</span>
</pre>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">minmapq=\-1 If non\-negative, toss reads with mapq under this.</span>
</pre>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">maxmapq=\-1 If non\-negative, toss reads with mapq over this.</span>
</pre>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">requiredbits=0 (rbits) Toss sam lines with any of these flag bits unset. Similar to samtools \fB\-f\fR.</span>
</pre>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">filterbits=0 (fbits) Toss sam lines with any of these flag bits set. Similar to samtools \fB\-F\fR.</span>
</pre>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">stoptag=f Set to true to write a tag indicating read stop location, prefixed by YS:i:</span>
</pre>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">sam= Set to 'sam=1.3' to convert '=' and 'X' cigar symbols (from sam 1.4+ format) to 'M'.</span>
</pre>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">.IP</span>
</pre>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">Set to 'sam=1.4' to convert 'M' to '=' and 'X' (sam=1.4 requires MD tags to be present, or ref to be specified).</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">.PP</span>
</pre>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">Sam and bam alignment filtering options:</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">These require = and X symbols in cigar strings, or MD tags, or areference fasta.</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">\fB\-1\fR means disabled; to filter reads with any of a symbol type, set to 0.</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">.PP</span>
</pre>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">subfilter=\-1 Discard reads with more than this many substitutions.</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">insfilter=\-1 Discard reads with more than this many insertions.</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">delfilter=\-1 Discard reads with more than this many deletions.</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">indelfilter=\-1 Discard reads with more than this many indels.</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">editfilter=\-1 Discard reads with more than this many edits.</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">inslenfilter=\-1 Discard reads with an insertion longer than this.</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">dellenfilter=\-1 Discard reads with a deletion longer than this.</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">idfilter=\-1.0 Discard reads with identity below this.</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">clipfilter=\-1 Discard reads with more than this many soft\-clipped bases.</span>
</pre>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">.PP</span>
</pre>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">Kmer counting and cardinality estimation:</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">k=0 If positive, count the total number of kmers.</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">cardinality=f (loglog) Count unique kmers using the LogLog algorithm.</span>
</pre>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">loglogbuckets=1999 Use this many buckets for cardinality estimation.</span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">.PP</span>
</pre>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">Shortcuts:</span>
</pre>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">The # symbol will be substituted for 1 and 2. The % symbol in out will be substituted for input name minus extensions.</span>
</pre>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">For example:</span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">reformat.sh in=read#.fq out=%.fa</span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">\&...is equivalent to:</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">reformat.sh in1=read1.fq in2=read2.fq out1=read1.fa out2=read2.fa</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">Java Parameters:</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">\fB\-Xmx\fR This will set Java's memory usage, overriding autodetection.</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">\fB\-Xmx20g\fR will specify 20 gigs of RAM, and \fB\-Xmx200m\fR will specify 200 megs.</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">The max is typically 85% of physical memory.</span>
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<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">\fB\-eoom\fR This flag will cause the process to exit if an out\-of\-memory exception occurs. Requires Java 8u92+.</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">\fB\-da\fR Disable assertions.</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">.SH AUTHOR</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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