files that hold the flashed reads.</p>
</div>
<div id="mappingaligning-the-reads" class="section level3">
<h3 class="hasAnchor">
<a href="#mappingaligning-the-reads" class="anchor"></a>Mapping/Aligning the Reads</h3>
<p>The reference sequences we will use to align to are in a fasta file called <code>gtseq15_loci.fasta</code>. We put that in the <code>map</code> directory and then commence mapping the flashed reads as follows:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode sh"><code class="sourc