the bioinformatics chat

A podcast about computational biology, bioinformatics, and next generation sequencing.

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episode 54: Seeding methods for read alignment with Markus Schmidt


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:

  • A performant bridge between fixed-size and variable-size seeding (Arne Kutzner, Pok-Son Kim, Markus Schmidt)
  • 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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 2020-12-16  1h0m