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. 2016 Nov 15;32(22):3507-3509.
doi: 10.1093/bioinformatics/btw490. Epub 2016 Jul 27.

WALT: fast and accurate read mapping for bisulfite sequencing

Haifeng Chen  1 , Andrew D Smith  1 , Ting Chen  1
Affiliations

WALT: fast and accurate read mapping for bisulfite sequencing

Haifeng Chen et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
Runtime as a function of read length
See this image and copyright information in PMC

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