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

the bioinformatics chat

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

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