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

Don't miss the next episode! Subscribe on Apple Podcasts, Google Podcasts, Spotify, or via the RSS feed link. You can also follow the podcast on Twitter and Mastodon.

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