WALT: fast and accurate read mapping for bisulfite sequencing
Open Access
- 27 July 2016
- journal article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 32 (22), 3507-3509
- https://doi.org/10.1093/bioinformatics/btw490
Abstract
Summary: 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 theWALT 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.Keywords
Funding Information
- National Institutes of Health (HG006015)
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