use-with-microhaplot" class="anchor"></a>What kind of data can I use with <code>microhaplot</code>?</h2>
<p>‘microhaplot’ is designed to work with short read sequencing data where there is a relatively small number sequencing start sites. It is emphatically <em>not</em> geared to whole-genome shotgun sequencing data in which you may have overlapping reads with different starting place. We use ‘microhaplot’ primarily with amplicon sequencing data in which a few hundred fragments (of about 100 - 150 b