In this episode, Markus Schmidt explains how seeding in read alignment works.

We define and compare k-mers, minimizers, MEMs, SMEMs, and maximal spanning seeds.

Markus also presents his recent work on computing variable-sized seeds (MEMs,

SMEMs, and maximal spanning seeds) from fixed-sized seeds (k-mers and

minimizers) and his Modular Aligner.

Links:

MA the Modular Aligner

Calibrating Seed-Based Heuristics to Map Short Reads With Sesame

(Guillaume J. Filion, Ruggero Cortini, Eduard Zorita) — another

interesting recent work on seeding methods (though we didn’t get to discuss

it in this episode)

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