Mikhail Kolmogorov's guest appearances

Mikhail Kolmogorov

the bioinformatics chat

David Kelley

Irineo Cabreros

Romain Lopez

Gabriel Misrachi

Hassan Samee

Kristina Grigaityte

Jacob Schreiber

Simeon Carstens

Trevor Pesout

HoJoon Lee

Seung Woo Cho

Kaushik Panda

Keith Slotkin

Fernando Portela

Chang Xu

OwlTail

Modern genome assembly projects are often based on long reads in an attempt tobridge longer repeats.  However, due to the higher error rate of the currentlong read sequencers, assemblers based on de Bruijn graphs do not work well inthis setting, and the approaches that do work are slower. In this episode, Mikhail Kolmogorov fromPavel Pevzner’s lab joins us to talk about some of the ideas developed in thelab that made it possible to build a de Bruijn-like assembly graph from noisyreads. These ideas are now implemented in the Flye assembler, which performsmuch faster than the existing long read assemblers without sacrificing thequality of the assembly. Links:  Assembly of Long Error-Prone Reads Using Repeat Graphs (Mikhail Kolmogorov,  Jeffrey Yuan, Yu Lin, Pavel. A. Pevzner.Nature Biotechnology(paywalled),bioRxiv Flye on GitHub  If you enjoyed this episode, please consider supporting the podcast on Patreon!

Modern genome assembly projects are often based on long reads in an attempt to bridge longer repeats. However, due to the higher error rate of the current long read sequencers, assemblers based on de Bruijn graphs do not work well in this setting, and the approaches that do work are slower. In this episode, <a href="https://twitter.com/fenderglass" rel="nofollow" target="_blank">Mikhail Kolmogorov</a> from Pavel Pevzner’s lab joins us to talk about some of the ideas developed in the lab that made it possible to build a de Bruijn-like assembly graph from noisy reads. These ideas are now implemented in the Flye assembler, which performs much faster than the existing long read assemblers without sacrificing the quality of the assembly. Links: <ul> <li>Assembly of Long Error-Prone Reads Using Repeat Graphs (Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel. A. Pevzner. <a href="https://www.nature.com/articles/s41587-019-0072-8" rel="nofollow" target="_blank">Nature Biotechnology</a> (paywalled), <a href="https://www.biorxiv.org/content/10.1101/247148v1" rel="nofollow" target="_blank">bioRxiv</a></li> <li><a href="https://github.com/fenderglass/Flye" rel="nofollow" target="_blank">Flye on GitHub</a></li> </ul> If you enjoyed this episode, please consider supporting the podcast on <a href="https://www.patreon.com/bioinfochat" rel="nofollow" target="_blank">Patreon</a>!

#33 Genome assembly from long reads and Flye with Mikhail Kolmogorov