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<title>1. Quick example — ProPhyle 0.3.3.2 documentation</title>
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<div style="color:white;font-size:240%">ProPhyle</div>
<div style="color:white;font-size:140%">DNA sequence classification</div>
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<section id="quick-example">
<span id="index-0"></span><span id="example"></span><h1><span class="section-number">1. </span>Quick example<a class="headerlink" href="#quick-example" title="Link to this heading">¶</a></h1>
<ol class="arabic">
<li><p>Install ProPhyle using <a class="reference external" href="https://bioconda.github.io/">Bioconda</a>:</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>defaults
conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>conda-forge
conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>bioconda
conda<span class="w"> </span>install<span class="w"> </span>prophyle
</pre></div>
</div>
</div></blockquote>
</li>
<li><p>Download the <a class="reference external" href="https://www.ncbi.nlm.nih.gov/refseq/">RefSeq</a> bacterial database:</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle<span class="w"> </span>download<span class="w"> </span>bacteria
</pre></div>
</div>
</div></blockquote>
</li>
<li><p>Build an index for randomly selected 10% genomes from the E.coli subtree (taxid 561 in the NCBI taxonomy), with k-mer size 25:</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle<span class="w"> </span>index<span class="w"> </span>-s<span class="w"> </span><span class="m">0</span>.10<span class="w"> </span>-k<span class="w"> </span><span class="m">25</span><span class="w"> </span>~/prophyle/bacteria.nw@561<span class="w"> </span>_index_ecoli
</pre></div>
</div>
</div></blockquote>
</li>
<li><p>Classify your reads:</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle<span class="w"> </span>classify<span class="w"> </span>_index_ecoli<span class="w"> </span>reads.fq<span class="w"> </span>><span class="w"> </span>result.sam
</pre></div>
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