BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.
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ABSTRACT: Summary
We introduce BRAT-BW, a fast, accurate and memory-efficient tool that maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-index (Burrows-Wheeler transform). BRAT-BW is significantly more memory efficient and faster on longer reads than current state-of-the-art tools for BS-seq data, without compromising on accuracy. BRAT-BW is a part of a software suite for genome-wide single base-resolution methylation data analysis that supports single and paired-end reads and includes a tool for estimation of methylation level at each cytosine.Availability
The software is available in the public domain at http://compbio.cs.ucr.edu/brat/.
SUBMITTER: Harris EY
PROVIDER: S-EPMC3381974 | biostudies-literature |
REPOSITORIES: biostudies-literature
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