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Haplotype threading: accurate polyploid phasing from long reads.

ABSTRACT: Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. Polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.We present WHATSHAP POLYPHASE, a novel two-stage approach that addresses these challenges by (i) clustering reads and (ii) threading the haplotypes through the clusters. Our method outperforms the state-of-the-art in terms of phasing quality. Using a real tetraploid potato dataset, we demonstrate how to assemble local genomic regions of interest at the haplotype level. Our algorithm is implemented as part of the widely used open source tool WhatsHap.

SUBMITTER: Schrinner SD

PROVIDER: S-EPMC7504856 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Haplotype threading: accurate polyploid phasing from long reads.

Schrinner Sven D SD Mari Rebecca Serra RS Ebler Jana J Rautiainen Mikko M Seillier Lancelot L Reimer Julia J JJ Usadel Björn B Marschall Tobias T Klau Gunnar W GW

Genome biology 20200921 1

Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. Polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.We present WHATSHAP POLYPHASE, a novel two-stage approach that addresses these challenges by (i) clustering reads and (ii) threading the haplotypes through the clusters. Our method outperforms the state-of-the-art in terms of phasing q ...[more]

PMID: 32951599

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