the bioinformatics chat

#29 Haplotype-aware genotyping from long reads with Trevor Pesout

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Long read sequencing technologies, such as Oxford Nanopore and PacBio,

produce reads from thousands to a million base pairs in length,
at the cost of the increased error rate. Trevor Pesout
describes how he and his colleagues leverage long reads for simultaneous
variant calling/genotyping and phasing. This is possible thanks to a clever
use of a hidden Markov model, and two different algorithms based on this model
are now implemented in
the MarginPhase and WhatsHap tools.

Links:

  • Preprint: Haplotype-aware genotyping from noisy long reads (Jana Ebler, Marina Haukness, Trevor Pesout, Tobias Marschall, Benedict Paten)

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