the bioinformatics chat

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

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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, Mikhail Kolmogorov 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:

  • 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

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