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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/megahit">Debian Med / megahit</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/megahit/commit/d72c2a0808ddcc96a2fe8a26e80d6b03c2133bb0">d72c2a08</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-10-10T23:49:22Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Manpages. Will refine the outputs soon
</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
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+
debian/manpages
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<li class="file-stats">
<a href="#f8030c8a2aa1cf9c7cbc77c8064afbc015b60190">
<span class="new-file">
+
debian/mans/megahit.1
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<li class="file-stats">
<a href="#46bbcee687a75c7a5688c2098367d984018c038d">
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+
debian/mans/megahit_core.1
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<li class="file-stats">
<a href="#ae713ad5c133afe5813b240a5f7b8f781953d2ab">
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debian/mans/megahit_core_no_hw_accel.1
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<li class="file-stats">
<a href="#407c225449d0d2815b39c1680a8734d06a87dc72">
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debian/mans/megahit_core_popcnt.1
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<li class="file-stats">
<a href="#1302d924773b5a9c29db9dda9a091bcc91d495f9">
<span class="new-file">
+
debian/mans/megahit_toolkit.1
</span>
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<h4>Changes:</h4>
<li id="68e0b13744e158347bfd74ebaaca667435f07d14">
<a href="https://salsa.debian.org/med-team/megahit/commit/d72c2a0808ddcc96a2fe8a26e80d6b03c2133bb0#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</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">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/mans/*.1</span></pre>
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<br>
</li>
<li id="f8030c8a2aa1cf9c7cbc77c8064afbc015b60190">
<a href="https://salsa.debian.org/med-team/megahit/commit/d72c2a0808ddcc96a2fe8a26e80d6b03c2133bb0#f8030c8a2aa1cf9c7cbc77c8064afbc015b60190"><strong>debian/mans/megahit.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH MEGAHIT "1" "October 2019" "megahit 1.2.8" "User Commands"</span>
</pre>
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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">
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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="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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">megahit \- ultra-fast and memory-efficient meta-genome assembler</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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
</pre>
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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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">MEGAHIT v1.2.8</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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.PP</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">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">contact: Dinghua Li <voutcn@gmail.com></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">.SS "Usage:"</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">.IP</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">megahit [options] {\-1 <pe1> \fB\-2\fR <pe2> | \fB\-\-12\fR <pe12> | \fB\-r\fR <se>} [\-o <out_dir>]</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">
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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">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Input options that can be specified for multiple times (supporting plain text and gz/bz2 extensions)</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">.TP</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">\fB\-1\fR</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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"><pe1> comma\-separated list of fasta/q paired\-end #1 files, paired with files in <pe2></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\-2\fR</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"><pe2> comma\-separated list of fasta/q paired\-end #2 files, paired with files in <pe1></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\-\-12\fR</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"><pe12> comma\-separated list of interleaved fasta/q paired\-end files</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-r\fR/\-\-read</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"><se> comma\-separated list of fasta/q single\-end files</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.SS "Optional Arguments:"</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.IP</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Basic assembly options:</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-\-min\-count\fR</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"><int> minimum multiplicity for filtering (k_min+1)\-mers [2]</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-\-k\-list\fR</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"><int,int,..> comma\-separated list of kmer size</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">all must be odd, in the range 15\-255, increment <= 28)</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">[21,29,39,59,79,99,119,141]</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.IP</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Another way to set \fB\-\-k\-list\fR (overrides \fB\-\-k\-list\fR if one of them set):</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-\-k\-min\fR</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"><int> minimum kmer size (<= 255), must be odd number [21]</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.TP</span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-\-k\-max\fR</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"><int> maximum kmer size (<= 255), must be odd number [141]</span>
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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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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">\fB\-\-k\-step\fR</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"><int> increment of kmer size of each iteration (<= 28), must be even number [12]</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">Advanced assembly options:</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.TP</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">\fB\-\-no\-mercy\fR</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">do not add mercy kmers</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.TP</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">\fB\-\-bubble\-level\fR</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"><int> intensity of bubble merging (0\-2), 0 to disable [2]</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.TP</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">\fB\-\-merge\-level\fR</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"><l,s> merge complex bubbles of length <= l*kmer_size and similarity >= s [20,0.95]</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.TP</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">\fB\-\-prune\-level\fR</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"><int> strength of low depth pruning (0\-3) [2]</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.TP</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">\fB\-\-prune\-depth\fR</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"><int> remove unitigs with avg kmer depth less than this value [2]</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.TP</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">\fB\-\-disconnect\-ratio\fR</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"><float> disconnect unitigs if its depth is less than this ratio times</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">the total depth of itself and its siblings [0.1]</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.TP</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">\fB\-\-low\-local\-ratio\fR</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"><float> remove unitigs if its depth is less than this ratio times</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">the average depth of the neighborhoods [0.2]</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">.TP</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">\fB\-\-max\-tip\-len\fR</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"><int> remove tips less than this value [2*k]</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">.TP</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">\fB\-\-cleaning\-rounds\fR</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"><int> number of rounds for graph cleanning [5]</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.TP</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">\fB\-\-no\-local\fR</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">disable local assembly</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">.TP</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">\fB\-\-kmin\-1pass\fR</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">use 1pass mode to build SdBG of k_min</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.IP</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">Presets parameters:</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.TP</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">\fB\-\-presets\fR</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"><str> override a group of parameters; possible values:</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">meta\-sensitive: '\-\-min\-count 1 \fB\-\-k\-list\fR 21,29,39,49,...,129,141'</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">meta\-large: '\-\-k\-min 27 \fB\-\-k\-max\fR 127 \fB\-\-k\-step\fR 10'</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">(large & complex metagenomes, like soil)</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">.IP</span>
</pre>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">Hardware options:</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">.TP</span>
</pre>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">\fB\-m\fR/\-\-memory</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"><float> max memory in byte to be used in SdBG construction</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">(if set between 0\-1, fraction of the machine's total memory) [0.9]</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">.TP</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">\fB\-\-mem\-flag\fR</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"><int> SdBG builder memory mode. 0: minimum; 1: moderate;</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">others: use all memory specified by '\-m/\-\-memory' [1]</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.TP</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">\fB\-t\fR/\-\-num\-cpu\-threads</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"><int> number of CPU threads [# of logical processors]</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.TP</span>
</pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">\fB\-\-no\-hw\-accel\fR</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">run MEGAHIT without BMI2 and POPCNT hardware instructions</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">.IP</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">Output options:</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">.TP</span>
</pre>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">\fB\-o\fR/\-\-out\-dir</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"><string> output directory [./megahit_out]</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">.TP</span>
</pre>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">\fB\-\-out\-prefix\fR</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"><string> output prefix (the contig file will be OUT_DIR/OUT_PREFIX.contigs.fa)</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">.TP</span>
</pre>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">\fB\-\-min\-contig\-len\fR</span>
</pre>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"><int> minimum length of contigs to output [200]</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">.TP</span>
</pre>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">\fB\-\-keep\-tmp\-files\fR</span>
</pre>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">keep all temporary files</span>
</pre>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">.TP</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">\fB\-\-tmp\-dir\fR</span>
</pre>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"><string> set temp directory</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">.SS "Other Arguments:"</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">.TP</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">\fB\-\-continue\fR</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">continue a MEGAHIT run from its last available check point.</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">please set the output directory correctly when using this option.</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">.TP</span>
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<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">\fB\-\-test\fR</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">run MEGAHIT on a toy test dataset</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">.TP</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">\fB\-h\fR/\-\-help</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">print the usage message</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">.TP</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">\fB\-v\fR/\-\-version</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">print version</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">.SH AUTHOR</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">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="46bbcee687a75c7a5688c2098367d984018c038d">
<a href="https://salsa.debian.org/med-team/megahit/commit/d72c2a0808ddcc96a2fe8a26e80d6b03c2133bb0#46bbcee687a75c7a5688c2098367d984018c038d"><strong>debian/mans/megahit_core.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH MEGAHIT_CORE "1" "October 2019" "megahit_core 1.2.8" "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">megahit_core \- ultra-fast and memory-efficient meta-genome assembler</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 megahit_core</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,<sub_program> \/\fR[\fI\,sub options\/\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">.IP</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">sub\-programs:</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.TP</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">assemble</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">assemble from SdBG</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">local</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">local asssembly</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">iterate</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">extract iterative edges</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">buildlib</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">build read library</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">count</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">kmer counting</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">read2sdbg</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">build sdbg from reads</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">seq2sdbg</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">build sdbg from megahit contigs + edges</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
</pre>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">contig2fastg</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">convert MEGAHIT's k*.contigs.fa to fastg format</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">readstat</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">calculate read stats (# of reads, bases, longest, shortest, average)</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">filterbylen</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">filter contigs by length</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">checkcpu</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">check whether the run\-time CPU supports POPCNT and BMI2</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.TP</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">checkpopcnt</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">check whether the run\-time CPU supports POPCNT</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">checkbmi2</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">check whether the run\-time CPU supports BMI2</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.TP</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">dumpversion</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">dump version</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.TP</span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">kmax</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">the largest k value supported</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="ae713ad5c133afe5813b240a5f7b8f781953d2ab">
<a href="https://salsa.debian.org/med-team/megahit/commit/d72c2a0808ddcc96a2fe8a26e80d6b03c2133bb0#ae713ad5c133afe5813b240a5f7b8f781953d2ab"><strong>debian/mans/megahit_core_no_hw_accel.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH MEGAHIT_CORE_NO_HW_ACCEL "1" "October 2019" "megahit_core_no_hw_accel 1.2.8" "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">megahit_core_no_hw_accel \- ultra-fast and memory-efficient meta-genome assembler</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 megahit_core_no_hw_accel</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,<sub_program> \/\fR[\fI\,sub options\/\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">.IP</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">sub\-programs:</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.TP</span>
</pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">assemble</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">assemble from SdBG</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">local</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">local asssembly</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">iterate</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">extract iterative edges</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">buildlib</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">build read library</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">count</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">kmer counting</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">read2sdbg</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">build sdbg from reads</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">seq2sdbg</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">build sdbg from megahit contigs + edges</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">contig2fastg</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">convert MEGAHIT's k*.contigs.fa to fastg format</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">readstat</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">calculate read stats (# of reads, bases, longest, shortest, average)</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">filterbylen</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">filter contigs by length</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">checkcpu</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">check whether the run\-time CPU supports POPCNT and BMI2</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.TP</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">checkpopcnt</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">check whether the run\-time CPU supports POPCNT</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">checkbmi2</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">check whether the run\-time CPU supports BMI2</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.TP</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">dumpversion</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">dump version</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.TP</span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">kmax</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">the largest k value supported</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="407c225449d0d2815b39c1680a8734d06a87dc72">
<a href="https://salsa.debian.org/med-team/megahit/commit/d72c2a0808ddcc96a2fe8a26e80d6b03c2133bb0#407c225449d0d2815b39c1680a8734d06a87dc72"><strong>debian/mans/megahit_core_popcnt.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH MEGAHIT_CORE_POPCNT "1" "October 2019" "megahit_core_popcnt 1.2.8" "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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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">megahit_core_popcnt \- ultra-fast and memory-efficient meta-genome assembler</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 megahit_core_popcnt</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,<sub_program> \/\fR[\fI\,sub options\/\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">.IP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">sub\-programs:</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.TP</span>
</pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">assemble</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">assemble from SdBG</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">local</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">local asssembly</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">iterate</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">extract iterative edges</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">buildlib</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">build read library</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">count</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">kmer counting</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">read2sdbg</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">build sdbg from reads</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">seq2sdbg</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">build sdbg from megahit contigs + edges</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">contig2fastg</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">convert MEGAHIT's k*.contigs.fa to fastg format</span>
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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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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">readstat</span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">calculate read stats (# of reads, bases, longest, shortest, average)</span>
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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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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">filterbylen</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">filter contigs by length</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">checkcpu</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">check whether the run\-time CPU supports POPCNT and BMI2</span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.TP</span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">checkpopcnt</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">check whether the run\-time CPU supports POPCNT</span>
</pre>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">checkbmi2</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">check whether the run\-time CPU supports BMI2</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.TP</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">dumpversion</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">dump version</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.TP</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">kmax</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">the largest k value supported</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="1302d924773b5a9c29db9dda9a091bcc91d495f9">
<a href="https://salsa.debian.org/med-team/megahit/commit/d72c2a0808ddcc96a2fe8a26e80d6b03c2133bb0#1302d924773b5a9c29db9dda9a091bcc91d495f9"><strong>debian/mans/megahit_toolkit.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH MEGAHIT_TOOLKIT "1" "October 2019" "megahit_toolkit 1.2.8" "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">megahit_toolkit \- ultra-fast and memory-efficient meta-genome assembler</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 megahit_toolkit</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,<sub_program> \/\fR[\fI\,sub options\/\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">.IP</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">sub\-programs:</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.TP</span>
</pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">assemble</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">assemble from SdBG</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">local</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">local asssembly</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">iterate</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">extract iterative edges</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">buildlib</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">build read library</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">count</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">kmer counting</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">read2sdbg</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">build sdbg from reads</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">seq2sdbg</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">build sdbg from megahit contigs + edges</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">contig2fastg</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">convert MEGAHIT's k*.contigs.fa to fastg format</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">readstat</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">calculate read stats (# of reads, bases, longest, shortest, average)</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">filterbylen</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">filter contigs by length</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">checkcpu</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">check whether the run\-time CPU supports POPCNT and BMI2</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.TP</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">checkpopcnt</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">check whether the run\-time CPU supports POPCNT</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">checkbmi2</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">check whether the run\-time CPU supports BMI2</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.TP</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">dumpversion</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">dump version</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.TP</span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">kmax</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">the largest k value supported</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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