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<li><a class="reference internal" href="#">4. Building a standard database</a><ul>
<li><a class="reference internal" href="#downloading-genomes">4.1. Downloading genomes</a></li>
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<section id="building-a-standard-database">
<span id="index-0"></span><span id="standard-db"></span><h1><span class="section-number">4. </span>Building a standard database<a class="headerlink" href="#building-a-standard-database" title="Link to this heading">¶</a></h1>
<p>ProPhyle comes with several genome libraries containing
RefSeq genomes, augmented with the NCBI taxonomy.</p>
<section id="downloading-genomes">
<h2><span class="section-number">4.1. </span>Downloading genomes<a class="headerlink" href="#downloading-genomes" title="Link to this heading">¶</a></h2>
<p>These libraries can be downloaded using <code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">download</span> <span class="pre"><library></span> <span class="pre">[<library></span> <span class="pre">...]</span></code>,
where <code class="docutils literal notranslate"><span class="pre"><library></span></code> should be replaced by <code class="docutils literal notranslate"><span class="pre">bacteria</span></code>, <code class="docutils literal notranslate"><span class="pre">viruses</span></code>, or <code class="docutils literal notranslate"><span class="pre">plasmids</span></code>.
The command also copies a prebuild Newick/NHX tree for the specified library.
If the <cite>-d</cite> parameter is not specified, all files are placed to <cite>~/prophyle</cite>.</p>
<p>To download all viral and bacterial genomes from RefSeq, execute</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle<span class="w"> </span>download<span class="w"> </span>bacteria<span class="w"> </span>viruses
</pre></div>
</div>
</section>
<section id="index-construction">
<h2><span class="section-number">4.2. </span>Index construction<a class="headerlink" href="#index-construction" title="Link to this heading">¶</a></h2>
<p>Once a library is downloaded, a ProPhyle index can be constructed using</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle<span class="w"> </span>index<span class="w"> </span><span class="o">[</span>-g<span class="w"> </span>DIR<span class="o">]</span><span class="w"> </span><span class="o">[</span>-j<span class="w"> </span>INT<span class="o">]</span><span class="w"> </span><span class="o">[</span>-k<span class="w"> </span>INT<span class="o">]</span><span class="w"> </span><span class="o">[</span>-M<span class="o">]</span><span class="w"> </span><span class="o">[</span>-P<span class="o">]</span><span class="w"> </span><span class="o">[</span>-K<span class="o">]</span><span class="w"> </span><tree.nw><span class="w"> </span><span class="o">[</span><tree.nw><span class="w"> </span>...<span class="o">]</span><span class="w"> </span><index.dir>
</pre></div>
</div>
<p><cite><tree.nw></cite> is a Newick/NHX for the index. The trees from the previous command
are placed in <cite>~/prophyle</cite> and they are called <cite>bacteria.nw</cite>, <cite>viruses.nw</cite>, etc.
<cite><index.dir></cite> is the directory directory where your index files are going to
be placed.</p>
<p>There are multiple other parameters that can be used.
<cite>-j</cite> can be used to specify the number of CPU cores used for index construction (all cores are used otherwise).
<cite>-k</cite> serves to set the <em>k</em>-mer length (31 in default).
<cite>-M</cite> activates low complexity regions filtering using DustMasker. Please, ensure that the program is install (try to run <cite>dustmasker</cite>).
If multiple trees are used, they are going to be merged. Therefore, a name collision can
appear. To prevent such a situation, ProPhyle prepends numerical prefixes to the
node names (unless <cite>-P</cite> is used).
The <cite>-K</cite> parameter can be used to deactivate <em>k</em>-LCP array construction. The resulting index
would be slightly smaller, but querying would become much slower.</p>
<p>So the entire command for index construction can look, for instance,
like this:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle<span class="w"> </span>index<span class="w"> </span>-k<span class="w"> </span><span class="m">25</span><span class="w"> </span>~/prophyle/bacteria.nw<span class="w"> </span>~/prophyle/viruses.nw<span class="w"> </span>my_BV_index
</pre></div>
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<p>Index construction might take several hours, based on the database size, <em>k</em> and the number
of used cores.</p>
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