Chromosome-length haplotypes with StrandPhaseR and Strand-seq

UBC Faculty Research and Publications

Chromosome-length haplotypes with StrandPhaseR and Strand-seq Hanlon, Vincent; Porubsky, David; Lansdorp, Peter

Abstract

Dense local haplotypes can now readily be extracted from long-read or droplet-based sequence data. However, these methods struggle to combine subchromosomal haplotype blocks into global chromosome-length haplotypes. Strand-seq is a single cell sequencing technique that uses read orientation to capture sparse global phase information by sequencing only one of two DNA strands for each parental homolog. In combination with dense local haplotypes from other technologies, Strand-seq data can be used to obtain complete chromosome-length phase information. In this chapter, we run the R package StrandPhaseR to phase SNVs using publicly-available sequence data for sample HG005 of the Genome in a Bottle project.

Item Metadata

Title	Chromosome-length haplotypes with StrandPhaseR and Strand-seq
Alternate Title	Phasing SNVs with Strand-seq
Creator	Hanlon, Vincent; Porubsky, David; Lansdorp, Peter
Contributor	BC Cancer Agency
Date Issued	2021
Description	Dense local haplotypes can now readily be extracted from long-read or droplet-based sequence data. However, these methods struggle to combine subchromosomal haplotype blocks into global chromosome-length haplotypes. Strand-seq is a single cell sequencing technique that uses read orientation to capture sparse global phase information by sequencing only one of two DNA strands for each parental homolog. In combination with dense local haplotypes from other technologies, Strand-seq data can be used to obtain complete chromosome-length phase information. In this chapter, we run the R package StrandPhaseR to phase SNVs using publicly-available sequence data for sample HG005 of the Genome in a Bottle project.
Subject	phasing; haplotype; Strand-seq; StrandPhaseR; Genome in a Bottle
Genre	Book Chapter; Preprint
Type	Text
Language	eng
Date Available	2022-01-19
Provider	Vancouver : University of British Columbia Library
Rights	Attribution-NonCommercial-NoDerivatives 4.0 International
DOI	10.14288/1.0406302
URI	http://hdl.handle.net/2429/80678
Affiliation	Medicine, Faculty of; Medical Genetics, Department of
Peer Review Status	Unreviewed
Scholarly Level	Faculty; Researcher; Postdoctoral
Rights URI	http://creativecommons.org/licenses/by-nc-nd/4.0/
Aggregated Source Repository	DSpace

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