n class="ex">bwa</span> mem -aM -v 3 -t 10 -R <span class="st">"@RG\tID:s</span><span class="va">${i}</span><span class="st">\tLB:amplicon\tPL:ILLUMINA\tSM:satro</span><span class="va">${i}</span><span class="st">"</span> ./gtseq15_loci ../flash/S<span class="va">${i}</span>.extendedFrags.fastq.gz  <span class="op">&gt;</span> ./satro_flashed_s<span class="va">${i}</span>_aln.sam<span class="kw">;</span> <span class="kw">done</span></span>
<span id="cb4-19"><a href="#cb4-19"></a></span>
<span id="cb4-20"><a