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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/graphbin">Debian Med / graphbin</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/graphbin/-/commit/8d66d9aec21603c40f2181165cd052dc4cd6f648">8d66d9ae</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-07-16T17:21:08+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Write manpage
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<h4>2 changed files:</h4>
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<a href="#582fc9bc86f289d3d3e175e83d6dbbbf34d6a7d4">
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debian/graphbin.manpages
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debian/mans/graphbin.1
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<h4>Changes:</h4>
<li id="582fc9bc86f289d3d3e175e83d6dbbbf34d6a7d4">
<a href="https://salsa.debian.org/med-team/graphbin/-/commit/8d66d9aec21603c40f2181165cd052dc4cd6f648#582fc9bc86f289d3d3e175e83d6dbbbf34d6a7d4"><strong>debian/graphbin.manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/mans/*.1</span></pre>
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<li id="c3cb711e2d6da54f822b4d4154a0790be1b7c2f6">
<a href="https://salsa.debian.org/med-team/graphbin/-/commit/8d66d9aec21603c40f2181165cd052dc4cd6f648#c3cb711e2d6da54f822b4d4154a0790be1b7c2f6"><strong>debian/mans/graphbin.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH GRAPHBIN "1" "July 2020" "graphbin" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">graphbin \- refined binning of metagenomic contigs using assembly graphs</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">usage: graphbin [\fI\,-h\/\fR] \fB\-\-assembler\fR \fI\,ASSEMBLER\/\fR \fB\-\-graph\fR \fI\,GRAPH\/\fR [\-\-paths \fI\,PATHS\/\fR]</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">\fB\-\-binned\fR \fI\,BINNED\/\fR \fB\-\-output\fR \fI\,OUTPUT\/\fR [\-\-prefix \fI\,PREFIX\/\fR]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-\-max_iteration \fI\,MAX_ITERATION\/\fR]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">[\-\-diff_threshold\fI\, DIFF_THRESHOLD\/\fR]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">GraphBin is a metagenomic contig binning tool that makes use of</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">the contig connectivity information from the assembly graph to bin contigs. It</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">utilizes the binning result of an existing binning tool and a label</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">propagation algorithm to correct mis\-binned contigs and predict the labels of</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">contigs which are discarded due to short length.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SS "optional arguments:"</span>
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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">.TP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-\-assembler\fR ASSEMBLER</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">name of the assembler used (SPAdes, SGA or MEGAHIT).</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">GraphBin supports Flye, Canu and Miniasm long\-read</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">assemblies as well.</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-\-graph\fR GRAPH</span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">path to the assembly graph file</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-\-paths\fR PATHS</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">path to the contigs.paths file</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</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="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-\-binned\fR BINNED</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="33" 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">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">path to the .csv file with the initial binning output</span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">from an existing tool</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</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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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-\-output\fR OUTPUT</span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">path to the output folder</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</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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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-\-prefix\fR PREFIX</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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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">prefix for the output file</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</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="42" 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">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-\-max_iteration\fR MAX_ITERATION</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">maximum number of iterations for label propagation</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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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">algorithm. [default: 100]</span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.TP</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="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">\fB\-\-diff_threshold\fR DIFF_THRESHOLD</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="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">difference threshold for label propagation algorithm.</span>
</pre>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">[default: 0.1]</span></pre>
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