bioinformatics chat

the bioinformatics chat

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

January 27, 2019

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.

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

This episode was recorded with Cast.