Search


	Podcast:		the bioinformatics chat
	Episode:		#54 Seeding methods for read alignment with Markus Schmidt
	Category:		Science & Medicine
	Duration:		01:00:46
	Publish Date:		2020-12-16 19:00:00
	Description:		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)
	Total Play:		0