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WALT: fast and accurate read mapping for bisulfite sequencing.

ABSTRACT: Whole-genome bisulfite sequencing (WGBS) has emerged as the gold-standard technique in genome-scale studies of DNA methylation. Mapping reads from WGBS requires unique considerations that make the process more time-consuming than in other sequencing applications. Typical WGBS data sets contain several hundred million reads, adding to this analysis challenge. We present the WALT tool for mapping WGBS reads. WALT uses a strategy of hashing periodic spaced seeds, which leads to significant speedup compared with the most efficient methods currently available. Although many existing WGBS mappers slow down with read length, WALT improves in speed. Importantly, these speed gains do not sacrifice accuracy.

Availability and implementation

WALT is available under the GPL v3 license, and downloadable from https://github.com/smithlabcode/walt.

Contact

andrewds@usc.edu or tingchen@usc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUBMITTER: Chen H

PROVIDER: S-EPMC5181568 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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WALT: fast and accurate read mapping for bisulfite sequencing.

Chen Haifeng H Smith Andrew D AD Chen Ting T

Bioinformatics (Oxford, England) 20160727 22

Whole-genome bisulfite sequencing (WGBS) has emerged as the gold-standard technique in genome-scale studies of DNA methylation. Mapping reads from WGBS requires unique considerations that make the process more time-consuming than in other sequencing applications. Typical WGBS data sets contain several hundred million reads, adding to this analysis challenge. We present the WALT tool for mapping WGBS reads. WALT uses a strategy of hashing periodic spaced seeds, which leads to significant speedup ...[more]

PMID: 27466624

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