es—or “microhaplotypes” in the parlance of some—from aligned sequences. Before we go further, it will be good to step back and confirm of what we are calling as a short-read haplotype, or a “microhaplotype” within the context of microhaplot.</p>
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<p><em>What is a microhaplotype?</em></p>
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<p>To define a microhaplotype you need to first define a reference point or position that a read might align to. Then, <code>microhaplot</code> can analyze the reads aligning at those p