WALT: fast and accurate read mapping for bisulfite sequencing

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.

http://bioinformatics.oxfordjournals.org/cgi/content/short/32/22/3507?rss=1

Source: Bioinformatics - November 28, 2016 Category: Bioinformatics Authors: Chen, H., Smith, A. D., Chen, T. Tags: SEQUENCE ANALYSIS Source Type: research

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