TY  - JOUR
AU  - Schrinner, Sven D.
AU  - Mari, Rebecca Serra
AU  - Ebler, Jana
AU  - Rautiainen, Mikko
AU  - Seillier, Lancelot
AU  - Reimer, Julia J.
AU  - Usadel, Björn
AU  - Marschall, Tobias
AU  - Klau, Gunnar W.
TI  - Haplotype threading: accurate polyploid phasing from long reads
JO  - Genome biology
VL  - 21
IS  - 1
SN  - 1474-760X
CY  - London
PB  - BioMed Central
M1  - FZJ-2021-01210
SP  - 252
PY  - 2020
N1  - Grant name:de.NBI - Etablierungsphase: Leistungszentrum GCBN – Deutsches BioGreenformatics-Netzwerk für Kulturpflanzen, BMBF 031A536C
AB  - 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.
LB  - PUB:(DE-HGF)16
C6  - 32951599
UR  - <Go to ISI:>//WOS:000574470900001
DO  - DOI:10.1186/s13059-020-02158-1
UR  - https://juser.fz-juelich.de/record/890802
ER  -