></span>
<span id="cb4-15"><a href="#cb4-15"></a></span>
<span id="cb4-16"><a href="#cb4-16"></a><span class="co"># map reads. for each input file, the output is named satro_flashed_s${i}_aln.sam</span></span>
<span id="cb4-17"><a href="#cb4-17"></a><span class="co"># Note the -R to insert appropriate read group header lines</span></span>
<span id="cb4-18"><a href="#cb4-18"></a><span class="ex">/map/--%</span> for i in <span class="dt">{1..384}</span><span class="kw">;</span> <span class="kw">do</span> <spa