{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T22:50:30Z","timestamp":1722725430705},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,7,1]]},"abstract":"Abstract<\/jats:title>\n 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\u2013Wheeler 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.<\/jats:p>\n Availability: The software is available in the public domain at http:\/\/compbio.cs.ucr.edu\/brat\/.<\/jats:p>\n Contact: \u00a0elenah@cs.ucr.edu<\/jats:p>\n Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts264","type":"journal-article","created":{"date-parts":[[2012,5,5]],"date-time":"2012-05-05T09:09:30Z","timestamp":1336208970000},"page":"1795-1796","source":"Crossref","is-referenced-by-count":70,"title":["BRAT-BW: efficient and accurate mapping of bisulfite-treated reads"],"prefix":"10.1093","volume":"28","author":[{"given":"Elena Y.","family":"Harris","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, 2Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA and 3INRA, MycSA UR 1264, 71 Avenue Edouard Bourlaux, BP81, 33883 Villenave d'Ornon Cedex, France"}]},{"given":"Nadia","family":"Ponts","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA and 3INRA, MycSA UR 1264, 71 Avenue Edouard Bourlaux, BP81, 33883 Villenave d'Ornon Cedex, France"},{"name":"1 Department of Computer Science, 2Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA and 3INRA, MycSA UR 1264, 71 Avenue Edouard Bourlaux, BP81, 33883 Villenave d'Ornon Cedex, France"}]},{"given":"Karine G.","family":"Le Roch","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA and 3INRA, MycSA UR 1264, 71 Avenue Edouard Bourlaux, BP81, 33883 Villenave d'Ornon Cedex, France"}]},{"given":"Stefano","family":"Lonardi","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA and 3INRA, MycSA UR 1264, 71 Avenue Edouard Bourlaux, BP81, 33883 Villenave d'Ornon Cedex, France"}]}],"member":"286","published-online":{"date-parts":[[2012,5,3]]},"reference":[{"key":"2023012512430921400_B1","volume-title":"A block sorting lossless data compression algorithm.","author":"Burrows","year":"1994"},{"key":"2023012512430921400_B2","first-page":"203","article-title":"BS Seeker: precise mapping for bisulfite sequencing. 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