BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.
| Autor: | Harris EY; Department of Computer Science, University of California, Riverside, CA 92521, USA. elenah@cs.ucr.edu, Ponts N, Le Roch KG, Lonardi S |
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| Jazyk: | angličtina |
| Zdroj: | Bioinformatics (Oxford, England) [Bioinformatics] 2012 Jul 01; Vol. 28 (13), pp. 1795-6. Date of Electronic Publication: 2012 May 03. |
| DOI: | 10.1093/bioinformatics/bts264 |
| Abstrakt: | 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/. |
| Databáze: | MEDLINE |
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