the bioinformatics chat

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

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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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    the bioinformatics chatBy Roman Cheplyaka
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