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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/mecat2">Debian Med / mecat2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mecat2/-/commit/ee5920bafc04a52d0b27b656cc98b9c36e67adbe">ee5920ba</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-07-03T18:20:33+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Write manpages
</pre>
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<h4>7 changed files:</h4>
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<li class="file-stats">
<a href="#ce029fae072f5c5c75deab9bf0e0a81e197f5a2e">
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debian/mans/fsa_assemble.1
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<li class="file-stats">
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debian/mans/fsa_ctg_bridge.1
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debian/mans/fsa_ol_filter.1
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debian/mans/fsa_rd_stat.1
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debian/mans/mecat.1
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debian/mans/mecat2pcan.1
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<li class="file-stats">
<a href="#92c73722753d78b3b9da553b77c8ccaf866712ee">
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debian/mecat2.manpages
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<h4>Changes:</h4>
<li id="ce029fae072f5c5c75deab9bf0e0a81e197f5a2e">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/ee5920bafc04a52d0b27b656cc98b9c36e67adbe#ce029fae072f5c5c75deab9bf0e0a81e197f5a2e"><strong>debian/mans/fsa_assemble.1</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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 1.47.16.</span>
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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="plaintext">.TH FSA_ASSEMBLE "1" "July 2020" "Constructs contigs from filtered overlaps and corrected reads." "User Commands"</span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">fsa_assemble \- Constructs contigs from filtered overlaps and corrected reads</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B fsa_assemble</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR] \fI\,filterd_overlaps\/\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Constructs contigs from filtered overlaps and corrected reads.</span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">\fB\-\-min_length\fR=\fI\,INT\/\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">minimum length of reads</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">default: 0</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">minimum identity of overlaps</span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">default: 0</span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">minimum aligned length of overlaps</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">default: 0</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.HP</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-\-min_contig_length\fR=\fI\,INT\/\fR</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.IP</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">minimum length of contigs</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">default: 500</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.HP</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-\-read_file\fR=\fI\,STRING\/\fR</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.IP</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">read filename</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">default: ""</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.HP</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.IP</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">default: ""</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.HP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-\-output_directory\fR=\fI\,STRING\/\fR</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.IP</span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">directory for output files</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">default: "."</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.HP</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-\-select_branch=\fR"no|best"</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.IP</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch</span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">default: "no"</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.HP</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-\-thread_size\fR=\fI\,INT\/\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.IP</span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">number of threads</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">default: 1</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.HP</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">\fB\-\-dump\fR=\fI\,INT\/\fR</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">for testing, dump intermediate files</span>
</pre>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">default: 0</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">\fB\-\-run_mode\fR=\fI\,INT\/\fR</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.IP</span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">for testing</span>
</pre>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">default: 4</span>
</pre>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">\fB\-\-lfc\fR</span>
</pre>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">deprecated, for testing</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">\fB\-\-remove_chimer\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="72" 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">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">deprecated, remove chimer node</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.PP</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">Usage: fsa_assemble [options] filterd_overlaps</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">.IP</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">filterd_overlaps</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">.IP</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">input filename</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">.HP</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">\fB\-\-min_length\fR=\fI\,INT\/\fR</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">.IP</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">minimum length of reads</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">default: 0</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.IP</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">minimum identity of overlaps</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">default: 0</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">.HP</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR</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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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">minimum aligned length of overlaps</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">default: 0</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">\fB\-\-min_contig_length\fR=\fI\,INT\/\fR</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">minimum length of contigs</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">default: 500</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">\fB\-\-read_file\fR=\fI\,STRING\/\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">read filename</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">default: ""</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"</span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.</span>
</pre>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">default: ""</span>
</pre>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">\fB\-\-output_directory\fR=\fI\,STRING\/\fR</span>
</pre>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">directory for output files</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">default: "."</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">\fB\-\-select_branch=\fR"no|best"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch</span>
</pre>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">default: "no"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">\fB\-\-thread_size\fR=\fI\,INT\/\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="122" 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">
122
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">number of threads</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">default: 1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="125" 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">
125
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">\fB\-\-dump\fR=\fI\,INT\/\fR</span>
</pre>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">.IP</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">for testing, dump intermediate files</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">default: 0</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">.HP</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">\fB\-\-run_mode\fR=\fI\,INT\/\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">.IP</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">for testing</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">default: 4</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">.HP</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">\fB\-\-lfc\fR</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="138" 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">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">deprecated, for testing</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">.HP</span>
</pre>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">\fB\-\-remove_chimer\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">.IP</span>
</pre>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">deprecated, remove chimer node</span></pre>
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<li id="f46c082c3f700902456519a90b4ea6a999750656">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/ee5920bafc04a52d0b27b656cc98b9c36e67adbe#f46c082c3f700902456519a90b4ea6a999750656"><strong>debian/mans/fsa_ctg_bridge.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 1.47.16.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH FSA_CTG_BRIDGE "1" "July 2020" "Bridge contigs" "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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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">fsa_ctg_bridge \- Bridge contigs</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 fsa_ctg_bridge</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR] \fI\,rawreads contigs read2ctg bridged_contigs\/\fR</span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Command line tool to bridge contigs.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">It takes the following parameters:</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.IP</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">rawreads</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> rawread file</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.IP</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">contigs</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.IP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> The contig file</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.IP</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">read2ctg</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.IP</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> The file containing overlaps between rawread and contigs</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.IP</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">bridged_contigs</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.IP</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> The output file</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.SH OPTIONS</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-\-ctg2ctg_file\fR=\fI\,STRING\/\fR</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">filename containing overlaps between contigs</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">default: ""</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.HP</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-\-read_min_length\fR=\fI\,INT\/\fR</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.IP</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">minimum rawread length</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">default: 10000</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.HP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-\-ctg_min_length\fR=\fI\,INT\/\fR</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.IP</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">minimum contig length</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">default: 500</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.HP</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-\-read2ctg_min_identity\fR=\fI\,DOUBLE\/\fR</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.IP</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">minimum identity of overlaps between rawreads and contigs</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">default: 80</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.HP</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-\-ctg2ctg_min_identity\fR=\fI\,DOUBLE\/\fR</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.IP</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">minimum identity of overlaps between contigs</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">default: 95</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.HP</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">\fB\-\-read2ctg_max_overhang\fR=\fI\,INT\/\fR</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.IP</span>
</pre>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">maximum overhang of overlaps between rawreads and contigs</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">default: 500</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.HP</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">\fB\-\-ctg2ctg_max_overhang\fR=\fI\,INT\/\fR</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.IP</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">maximum overhang of overlaps between contigs</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">default: 100</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.HP</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">\fB\-\-read2ctg_min_aligned_length\fR=\fI\,INT\/\fR</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="69" 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">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">minimum aligned length of overlaps between rawreads and contigs</span>
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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">default: 5000</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.HP</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">\fB\-\-ctg2ctg_min_aligned_length\fR=\fI\,INT\/\fR</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">.IP</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">minimum aligned length of overlaps between contigs</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">default: 2000</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">.HP</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">\fB\-\-read2ctg_min_coverage\fR=\fI\,INT\/\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">minimum coverage of links between rawreads and contigs</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">default: 4</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">\fB\-\-min_contig_length\fR=\fI\,INT\/\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">minimum length of bridged contig</span>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">default: 500</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">\fB\-\-output_directory\fR=\fI\,STRING\/\fR</span>
</pre>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">.IP</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">directory for output files</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">default: "."</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">.HP</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">\fB\-\-select_branch=\fR"no|best"</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">selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">default: "no"</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">.HP</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">\fB\-\-dump\fR</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">.IP</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">for testing, dump intermediate files</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">.HP</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">\fB\-\-thread_size\fR=\fI\,INT\/\fR</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">.IP</span>
</pre>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">number of threads</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">default: 4</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">Usage: fsa_ctg_bridge [options] rawreads contigs read2ctg bridged_contigs</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">.IP</span>
</pre>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">rawreads</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">.IP</span>
</pre>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">rawread file</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">.IP</span>
</pre>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">contigs</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">.IP</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">contig file</span>
</pre>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">.IP</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">read2ctg</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">.IP</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">file containing overlaps between rawread and contigs</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">.IP</span>
</pre>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">bridged_contigs</span>
</pre>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">.IP</span>
</pre>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">output file</span>
</pre>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">.HP</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">\fB\-\-ctg2ctg_file\fR=\fI\,STRING\/\fR</span>
</pre>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">filename containing overlaps between contigs</span>
</pre>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">default: ""</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">\fB\-\-read_min_length\fR=\fI\,INT\/\fR</span>
</pre>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">minimum rawread length</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">default: 10000</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="133" 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">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="134" 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">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">\fB\-\-ctg_min_length\fR=\fI\,INT\/\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">minimum contig length</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">default: 500</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="138" 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">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="139" 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">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">\fB\-\-read2ctg_min_identity\fR=\fI\,DOUBLE\/\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">minimum identity of overlaps between rawreads and contigs</span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">default: 80</span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">\fB\-\-ctg2ctg_min_identity\fR=\fI\,DOUBLE\/\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">minimum identity of overlaps between contigs</span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">default: 95</span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">\fB\-\-read2ctg_max_overhang\fR=\fI\,INT\/\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">maximum overhang of overlaps between rawreads and contigs</span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">default: 500</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">\fB\-\-ctg2ctg_max_overhang\fR=\fI\,INT\/\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">maximum overhang of overlaps between contigs</span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">default: 100</span>
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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">\fB\-\-read2ctg_min_aligned_length\fR=\fI\,INT\/\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">minimum aligned length of overlaps between rawreads and contigs</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">default: 5000</span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="164" 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">
164
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">\fB\-\-ctg2ctg_min_aligned_length\fR=\fI\,INT\/\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">minimum aligned length of overlaps between contigs</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">default: 2000</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">.HP</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">\fB\-\-read2ctg_min_coverage\fR=\fI\,INT\/\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">minimum coverage of links between rawreads and contigs</span>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">default: 4</span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">\fB\-\-min_contig_length\fR=\fI\,INT\/\fR</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">minimum length of bridged contig</span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">default: 500</span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">.HP</span>
</pre>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">\fB\-\-output_directory\fR=\fI\,STRING\/\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="180" 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">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">.IP</span>
</pre>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">directory for output files</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">default: "."</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">\fB\-\-select_branch=\fR"no|best"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch</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">default: "no"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">\fB\-\-dump\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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">for testing, dump intermediate files</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">.HP</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">\fB\-\-thread_size\fR=\fI\,INT\/\fR</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">.IP</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">number of threads</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">default: 4</span></pre>
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<a href="https://salsa.debian.org/med-team/mecat2/-/commit/ee5920bafc04a52d0b27b656cc98b9c36e67adbe#9e80d74af035455a13c8a7bdf509ad6469a2250b"><strong>debian/mans/fsa_ol_filter.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 1.47.16.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH FILTERS "1" "July 2020" "Filters out low-quality overlaps for assembling" "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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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Filters \- Low quality overlap filtering</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 fsa_ol_filter</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR] \fI\,overlaps filtered_overlaps\/\fR</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Command line tool to filters out low\-quality overlaps prior to assembling.</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">This takes the following parameters:</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.IP</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">overlaps</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.IP</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> The input filename</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">filtered_overlaps</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.IP</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> The resulting ouput filename</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.SH OPTIONS</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.HP</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-\-min_length\fR=\fI\,INT\/\fR</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.IP</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">minimum length of reads</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.IP</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">default: 2500</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-\-max_length\fR=\fI\,INT\/\fR</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">maximum length of reads</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">default: 2147483647</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.IP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">minimum identity of overlaps</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">default: 90</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">minimum aligned length of overlaps</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">default: 2500</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">\fB\-\-max_overhang\fR=\fI\,INT\/\fR</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.IP</span>
</pre>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">maximum overhang of overlaps, negative number = determined by the program.</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.IP</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">default: 10</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.HP</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">\fB\-\-min_coverage\fR=\fI\,INT\/\fR</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.IP</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">minimum base coverage, negative number = determined by the program.</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">default: \fB\-1\fR</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.HP</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">\fB\-\-max_coverage\fR=\fI\,INT\/\fR</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.IP</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">maximum base coverage, negative number = determined by the program</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">default: \fB\-1\fR</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.HP</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">\fB\-\-max_diff_coverage\fR=\fI\,INT\/\fR</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.IP</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">maximum difference of base coverage, negative number = determined by the program</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">default: \fB\-1\fR</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.HP</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">\fB\-\-coverage_discard\fR=\fI\,DOUBLE\/\fR</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">discard ratio of base coverage. If max_coverage or max_diff_coverage is negative, it will be reset to (100\-coverage_discard)th percentile.</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">default: 0.01</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.HP</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">.IP</span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">default: ""</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.HP</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">\fB\-\-bestn\fR=\fI\,INT\/\fR</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">.IP</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">output best n overlaps on 5' or 3' end for each read</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.IP</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">default: 10</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">.HP</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">\fB\-\-genome_size\fR=\fI\,INT\/\fR</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">genome size. It determines the maximum length of reads with coverage together</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">default: 0</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">.HP</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">\fB\-\-coverage\fR=\fI\,INT\/\fR</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">.IP</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">coverage. It determines the maximum length of reads with genome_size together</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">default: 0</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">.HP</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">\fB\-\-output_directory\fR=\fI\,STRING\/\fR</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">directory for output files</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">default: "."</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">.HP</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">\fB\-\-thread_size\fR=\fI\,INT\/\fR</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">.IP</span>
</pre>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">number of threads</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">default: 4</span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">.PP</span>
</pre>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">Usage: fsa_ol_filter [options] overlaps filtered_overlaps</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">overlaps</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">input filename</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">filtered_overlaps</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">ouput filename</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">\fB\-\-min_length\fR=\fI\,INT\/\fR</span>
</pre>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">minimum length of reads</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">default: 2500</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">\fB\-\-max_length\fR=\fI\,INT\/\fR</span>
</pre>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">maximum length of reads</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">default: 2147483647</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">.IP</span>
</pre>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">minimum identity of overlaps</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">.IP</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">default: 90</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">.HP</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">.IP</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">minimum aligned length of overlaps</span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">default: 2500</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">.HP</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">\fB\-\-max_overhang\fR=\fI\,INT\/\fR</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">.IP</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">maximum overhang of overlaps, negative number = determined by the program.</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">default: 10</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">.HP</span>
</pre>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">\fB\-\-min_coverage\fR=\fI\,INT\/\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">minimum base coverage, negative number = determined by the program.</span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">default: \fB\-1\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">\fB\-\-max_coverage\fR=\fI\,INT\/\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">maximum base coverage, negative number = determined by the program</span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">default: \fB\-1\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">\fB\-\-max_diff_coverage\fR=\fI\,INT\/\fR</span>
</pre>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">.IP</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">maximum difference of base coverage, negative number = determined by the program</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">default: \fB\-1\fR</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">.HP</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">\fB\-\-coverage_discard\fR=\fI\,DOUBLE\/\fR</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">.IP</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">discard ratio of base coverage. If max_coverage or max_diff_coverage is negative, it will be reset to (100\-coverage_discard)th percentile.</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">default: 0.01</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">.HP</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">.IP</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">default: ""</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">.HP</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">\fB\-\-bestn\fR=\fI\,INT\/\fR</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">.IP</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">output best n overlaps on 5' or 3' end for each read</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">.IP</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">default: 10</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">.HP</span>
</pre>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">\fB\-\-genome_size\fR=\fI\,INT\/\fR</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">genome size. It determines the maximum length of reads with coverage together</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">default: 0</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">.HP</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">\fB\-\-coverage\fR=\fI\,INT\/\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">coverage. It determines the maximum length of reads with genome_size together</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">default: 0</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">.HP</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">\fB\-\-output_directory\fR=\fI\,STRING\/\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">directory for output files</span>
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<td class="diff-line-num new new_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">default: "."</span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">.HP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">\fB\-\-thread_size\fR=\fI\,INT\/\fR</span>
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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">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">number of threads</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">default: 4</span></pre>
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<li id="841adb3a078c77931b457eb8d15f38aed4dc123b">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/ee5920bafc04a52d0b27b656cc98b9c36e67adbe#841adb3a078c77931b457eb8d15f38aed4dc123b"><strong>debian/mans/fsa_rd_stat.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 1.47.16.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH FSA_RD_STAT "1" "July 2020" "fsa_rd_stat " "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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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">fsa_rd_stat \- Reads and outputs the filename of the dataset</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">fsa_rd_stat</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.B [options]</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">\fI\,ifname\/\fR</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.IP</span>
</pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">ifname</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.IP</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">read file name</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.SH OPTIONS</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.HP</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-\-thread_size\fR=\fI\,INT\/\fR</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Number of threads</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">default: 4</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.PP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Usage: [options] ifname</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.IP</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">ifname</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.IP</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">read file name</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.HP</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-\-thread_size\fR=\fI\,INT\/\fR</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.IP</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Number of threads</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">default: 4</span></pre>
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<a href="https://salsa.debian.org/med-team/mecat2/-/commit/ee5920bafc04a52d0b27b656cc98b9c36e67adbe#baeaa852c12df3e927d5ff1918fe537ec8d1a086"><strong>debian/mans/mecat.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 1.47.16.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH MECAT "1" "July 2020" "mecat" "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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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">mecat \- Generate config file or assemble, trim or correct SMRT data</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 mecat</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,correct|assemble|config cfg_fname\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">MECAT (v2) is an ultra-fast and accurate mapping, error correcting and de novo assembly tools for single molecula sequencing (SMRT) reads.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">The parameters are defined as below:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">correct:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Correct rawreads</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">trim:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Trim corrected reads</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">assemble:</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Generate contigs</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">config:</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> Generate default config file</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/mecat2/-/commit/ee5920bafc04a52d0b27b656cc98b9c36e67adbe#88c0848cd27ca502bb1fa1fda683a3ba95308c5a"><strong>debian/mans/mecat2pcan.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 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH MECAT2PCAN "1" "July 2020" "mecat2pcan" "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">mecat2pcan \- Partition consensus hits into smaller parts</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">mecat2pcan [\fI\,options\/\fR] \fI\,seqdb_dir \/\fR \fI\,pcan_dir \/\fR \fI\,cns_hits\/\fR</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.SH DESCRIPTION</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Command line tool to partition consensus hits into small parts</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SS "OPTIONAL ARGUMENTS:"</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-p\fR <Integer, >0></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Number of reads in each part</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Default = '100000'</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.HP</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-k\fR <Integer, >0></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Number of parts processed at each round</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">(If <0, then it will be set to system limit value)</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Default = '100'</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.HP</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-t\fR <Integer, >0></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Number of CPU threads</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Default = '1'</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/mans/*.1</span></pre>
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