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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/nanofilt">Debian Med / nanofilt</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/nanofilt/-/commit/987790d41c2a7b6ee0d871f1737827c086708498">987790d4</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-06-16T18:40:31+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpages
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<h4>2 changed files:</h4>
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<a href="#203cb61697afeeb4206ce35f1dfbbe21f98bb2ef">
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debian/mans/NanoFilt.1
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+
debian/nanofilt.manpages
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<h4>Changes:</h4>
<li id="203cb61697afeeb4206ce35f1dfbbe21f98bb2ef">
<a href="https://salsa.debian.org/med-team/nanofilt/-/commit/987790d41c2a7b6ee0d871f1737827c086708498#203cb61697afeeb4206ce35f1dfbbe21f98bb2ef"><strong>debian/mans/NanoFilt.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 NANOFILT "1" "June 2020" "NanoFilt 2.6.0" "User Commands"</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">NanoFilt \- filtering and trimming of long read sequencing data</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">usage: NanoFilt [\-h] [\-v] [\-\-logfile LOGFILE] [\-l LENGTH]</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.IP</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">[\-\-maxlength MAXLENGTH] [\-q QUALITY] [\-\-minGC MINGC]</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">[\-\-maxGC MAXGC] [\-\-headcrop HEADCROP] [\-\-tailcrop TAILCROP]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[\-s SUMMARY] [\-\-readtype {1D,2D,1D2}]</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">[input]</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">.PP</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">Perform quality and/or length and/or GC filtering of (long read) fastq data. Reads on stdin.</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">.SS "General options:"</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">.TP</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">\fB\-h\fR, \fB\-\-help\fR</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">show the help and exit</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</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">\fB\-v\fR, \fB\-\-version\fR</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Print version and exit.</span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-\-logfile\fR LOGFILE</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Specify the path and filename for the log file.</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">input</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">input, uncompressed fastq file</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.SS "Options for filtering reads on.:"</span>
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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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<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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-l\fR LENGTH, \fB\-\-length\fR LENGTH</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Filter on a minimum read length</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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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-\-maxlength\fR MAXLENGTH</span>
</pre>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Filter on a maximum read length</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" 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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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-q\fR QUALITY, \fB\-\-quality\fR QUALITY</span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Filter on a minimum average read quality score</span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" 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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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-\-minGC\fR MINGC</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Sequences must have GC content >= to this. Float between 0.0 and 1.0. Ignored if</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">using summary file.</span>
</pre>
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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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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-\-maxGC\fR MAXGC</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">Sequences must have GC content <= to this. Float between 0.0 and 1.0. Ignored if</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">using summary file.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.SS "Options for trimming reads.:"</span>
</pre>
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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">.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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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-\-headcrop\fR HEADCROP</span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Trim n nucleotides from start of read</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.TP</span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">\fB\-\-tailcrop\fR TAILCROP</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Trim n nucleotides from end of read</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.SS "Input options.:"</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\-s\fR SUMMARY, \fB\-\-summary\fR SUMMARY</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Use albacore or guppy summary file for quality scores</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\-\-readtype\fR {1D,2D,1D2}</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">Which read type to extract information about from summary. Options are 1D, 2D or</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">1D2</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.SS "EXAMPLES:"</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.IP</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">gunzip \fB\-c\fR reads.fastq.gz | NanoFilt \fB\-q\fR 10 \fB\-l\fR 500 \fB\-\-headcrop\fR 50 | minimap2 genome.fa \- | samtools sort \fB\-O\fR BAM \-@24 \fB\-o\fR alignment.bam \-</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">gunzip \fB\-c\fR reads.fastq.gz | NanoFilt \fB\-q\fR 12 \fB\-\-headcrop\fR 75 | gzip > trimmed\-reads.fastq.gz</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">gunzip \fB\-c\fR reads.fastq.gz | NanoFilt \fB\-q\fR 10 | gzip > highQuality\-reads.fastq.gz</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.SH "SEE ALSO"</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">The full documentation for</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.B NanoFilt</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">is maintained as a Texinfo manual. If the</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.B info</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">and</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.B NanoFilt</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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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">programs are properly installed at your site, the command</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">.IP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.B info NanoFilt</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">should give you access to the complete manual.</span></pre>
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<a href="https://salsa.debian.org/med-team/nanofilt/-/commit/987790d41c2a7b6ee0d871f1737827c086708498#012292688167c68c3e2aefcc5643a344cbbf3fb3"><strong>debian/nanofilt.manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/mans/*.1</span></pre>
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