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<section id="classifying-reads">
<span id="classify"></span><h1><span class="section-number">6. </span>Classifying reads<a class="headerlink" href="#classifying-reads" title="Link to this heading">¶</a></h1>
<p>When the index construction is finished, you can classify your reads using</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle<span class="w"> </span>classify<span class="w"> </span><index_dir><span class="w"> </span><reads.fq>
</pre></div>
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<p>For the index from above, the command would be:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle<span class="w"> </span>classify<span class="w"> </span>my_BV_index<span class="w"> </span>my_reads.fq
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<p>The assignments are reported in the SAM format.
Unless specified otherwise, the <em>k</em>-mer length is deduced from the index.</p>
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