 the reads together</h3>
<p>Our data are paired end reads of fragments that are short enough that the primary reads and the paired-end reads overlap. Rather than treat them as two separate reads, we combine them together into a single read using <a href="https://ccb.jhu.edu/software/FLASH/">flash</a>. Here is the command we use to cycle over all the files and flash them, run from the <code>flash</code> directory which is at the same level as the <code>rawdata</code> directory. (Note that the <code>/flash/--