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001     890802
005     20230111074330.0
024 7 _ |a 10.1186/s13059-020-02158-1
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100 1 _ |a Schrinner, Sven D.
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245 _ _ |a Haplotype threading: accurate polyploid phasing from long reads
260 _ _ |a London
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500 _ _ |a Grant name:de.NBI - Etablierungsphase: Leistungszentrum GCBN – Deutsches BioGreenformatics-Netzwerk für Kulturpflanzen, BMBF 031A536C
520 _ _ |a 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.
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700 1 _ |a Mari, Rebecca Serra
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700 1 _ |a Ebler, Jana
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700 1 _ |a Rautiainen, Mikko
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700 1 _ |a Seillier, Lancelot
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700 1 _ |a Reimer, Julia J.
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700 1 _ |a Usadel, Björn
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700 1 _ |a Marschall, Tobias
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700 1 _ |a Klau, Gunnar W.
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773 _ _ |a 10.1186/s13059-020-02158-1
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