Spectrum-preserving string sets and simplitigs with Amatur Rahman and Karel Břinda (#42)

February 28, 2020

In this episode, we hear from Amatur Rahman and Karel Břinda, who independently of one another released preprints on the same concept, called simplitigs or spectrum-preserving string sets. Simplitigs offer a way to efficiently store and query large sets of k-mers—or, equivalently, large de Bruijn graphs.

Links:

• Simplitigs as an efficient and scalable representation of de Bruijn graphs (Karel Břinda, Michael Baym, Gregory Kucherov)
• Representation of k-mer sets using spectrum-preserving string sets (Amatur Rahman, Paul Medvedev)
• Open mic

Music: Eric Skiff — Come and Find Me (modified, licensed under CC BY 4.0).

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