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. 2012 Jul 1;28(13):1795-6.
doi: 10.1093/bioinformatics/bts264. Epub 2012 May 3.

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads

Elena Y Harris  1 , Nadia Ponts, Karine G Le Roch, Stefano Lonardi
Affiliations

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads

Elena Y Harris et al. Bioinformatics. .

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/.

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Figures

Fig. 1.
Fig. 1.
Percentage of bases mapped uniquely (bars) and mapping accuracy (lines) on synthetic data, as a function of the read length
See this image and copyright information in PMC

References

    1. Burrows M., Wheeler D. A block sorting lossless data compression algorithm. 1994. Technical Report #124. Digital Equipment Corporation.
    1. Chen P.Y., et al. BS Seeker: precise mapping for bisulfite sequencing. BMC. Bioinform. 2010;11:203. - PMC - PubMed
    1. Cokus S.J., et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452:215–219. - PMC - PubMed
    1. Ferragina P., Manzini G. Proceedings of IEEE Foundation of Computer Science. Redondo Beach, CA: 2000. Opportunistic data structures with applications; pp. 390–398.
    1. Frommer M., et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. PNAS USA. 1992;89:1827–1831. - PMC - PubMed

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