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 Pesoutdescribes how he and his colleagues leverage long reads for simultaneousvariant calling/genotyping and phasing. This is possible thanks to a cleveruse of a hidden Markov model, and two different algorithms based on this modelare now implemented inthe MarginPhase and WhatsHap tools.

Links:

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