ata. Each step is described in one of the following subsections.</p>
<div id="starting-state" class="section level3">
<h3 class="hasAnchor">
<a href="#starting-state" class="anchor"></a>Starting state</h3>
<p>Out description starts at the point where we have copied all of our fastq.gz files from the sequencer into a directory called <code>rawdata</code>. Next to that directory we have made two more directories, <code>flash</code> and <code>map</code>, in which we will be creating files and doing work. We ha