h-bwa"><i class="fa fa-check"></i><b>19.3</b> Aligning reads with <code>bwa</code></a>
<ul>
<li class="chapter" data-level="19.3.1" data-path="alignment-of-sequence-data-to-a-reference-genome-and-associated-steps.html"><a href="alignment-of-sequence-data-to-a-reference-genome-and-associated-steps.html#indexing-the-genome-for-alignment"><i class="fa fa-check"></i><b>19.3.1</b> Indexing the genome for alignment</a></li>
<li class="chapter" data-level="19.3.2" data-path="alignment-of-sequence-data-to-a-referen