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Methods in molecular biology (Clifton, N.J.)
2023;2590 183-200.

Chromosome-Length Haplotypes with StrandPhaseR and Strand-seq.

Vincent C T Hanlon, David Porubsky, Peter M Lansdorp
Author Information
  1. Vincent C T Hanlon: Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada. vhanlon@bccrc.ca.
  2. David Porubsky: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. porubsky@uw.edu.
  3. Peter M Lansdorp: Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada.
PMID: 36335500 DOI: 10.1007/978-1-0716-2819-5_12

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.

Keywords

Genome in a Bottle Haplotype Phasing Strand-seq StrandPhaseR

References

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Grants

  1. PJT-159787/CIHR

MeSH Term

Haplotypes
Sequence Analysis, DNA
Chromosomes
Genome
High-Throughput Nucleotide Sequencing
Polymorphism, Single Nucleotide
Algorithms
Journal Article Research Support, Non-U.S. Gov't

Word Cloud

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