Universität zu Köln

Schrinner, Sven D., Mari, Rebecca Serra, Ebler, Jana, Rautiainen, Mikko, Seillier, Lancelot, Reimer, Julia J., Usadel, Bjoern, Marschall, Tobias and Klau, Gunnar W. (2020). Haplotype threading: accurate polyploid phasing from long reads. Genome Biol., 21 (1). LONDON: BMC. ISSN 1474-760X

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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 presentWhatsHap 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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Schrinner, Sven D. UNSPECIFIED UNSPECIFIED UNSPECIFIED Mari, Rebecca Serra UNSPECIFIED UNSPECIFIED UNSPECIFIED Ebler, Jana UNSPECIFIED UNSPECIFIED UNSPECIFIED Rautiainen, Mikko UNSPECIFIED UNSPECIFIED UNSPECIFIED Seillier, Lancelot UNSPECIFIED UNSPECIFIED UNSPECIFIED Reimer, Julia J. UNSPECIFIED UNSPECIFIED UNSPECIFIED Usadel, Bjoern UNSPECIFIED UNSPECIFIED UNSPECIFIED Marschall, Tobias UNSPECIFIED UNSPECIFIED UNSPECIFIED Klau, Gunnar W. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-318707
DOI:	10.1186/s13059-020-02158-1
Journal or Publication Title:	Genome Biol.
Volume:	21
Number:	1
Date:	2020
Publisher:	BMC
Place of Publication:	LONDON
ISSN:	1474-760X
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language ALGORITHMS; DIPLOIDS; GENOME Multiple languages Biotechnology & Applied Microbiology; Genetics & Heredity Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/31870