{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T06:29:54Z","timestamp":1771482594902,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We present a new, accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. Our tool, BRAT, supports single and paired-end reads and handles input files containing reads and mates of different lengths. BRAT is faster, maps more unique paired-end reads and has higher accuracy than existing programs. The software package includes tools to end-trim low-quality bases of the reads and to report nucleotide counts for mapped reads on the reference genome.<\/jats:p>\n               <jats:p>Availability: The source code is freely available for download at http:\/\/compbio.cs.ucr.edu\/brat\/ and is distributed as Open Source software under the GPLv3.0.<\/jats:p>\n               <jats:p>Contact: \u00a0elenah@cs.ucr.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp706","type":"journal-article","created":{"date-parts":[[2009,12,24]],"date-time":"2009-12-24T01:52:12Z","timestamp":1261619532000},"page":"572-573","source":"Crossref","is-referenced-by-count":62,"title":["BRAT: bisulfite-treated reads analysis tool"],"prefix":"10.1093","volume":"26","author":[{"given":"Elena Y.","family":"Harris","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, 2 Department of Cell Biology and Neuroscience and 3 Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Nadia","family":"Ponts","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2 Department of Cell Biology and Neuroscience and 3 Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Aleksandr","family":"Levchuk","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2 Department of Cell Biology and Neuroscience and 3 Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Karine Le","family":"Roch","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2 Department of Cell Biology and Neuroscience and 3 Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]},{"given":"Stefano","family":"Lonardi","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2 Department of Cell Biology and Neuroscience and 3 Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,12,22]]},"reference":[{"key":"2023012508021896400_B1","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nature06745","article-title":"Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning","volume":"452","author":"Cokus","year":"2008","journal-title":"Nature"},{"key":"2023012508021896400_B2","doi-asserted-by":"crossref","first-page":"1827","DOI":"10.1073\/pnas.89.5.1827","article-title":"A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands","volume":"89","author":"Frommer","year":"1992","journal-title":"Proc. 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