Journal Article

FZJ-2021-01210

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Haplotype threading: accurate polyploid phasing from long reads

Schrinner, S. D. ; Mari, R. S. ; Ebler, J. ; Rautiainen, M. ; Seillier, L. ; Reimer, J. J.FZJ* ; Usadel, B.FZJ* ; Marschall, T. (Corresponding author) ; Klau, G. W.Extern*

2020
BioMed Central London

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Please use a persistent id in citations: http://hdl.handle.net/2128/27274  doi:10.1186/s13059-020-02158-1

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.

Note: Grant name:de.NBI - Etablierungsphase: Leistungszentrum GCBN – Deutsches BioGreenformatics-Netzwerk für Kulturpflanzen, BMBF 031A536C

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Contributing Institute(s):

1. Bioinformatik (IBG-4)

Research Program(s):

1. 899 - ohne Topic (POF3-899) (POF3-899)

Appears in the scientific report 2021

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