{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T11:05:31Z","timestamp":1763809531668},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: In response to increasing amounts of sequencing data, faster and faster aligners need to become available. Here, we introduce BRAT-nova, a completely rewritten and improved implementation of the mapping tool BRAT-BW for bisulfite-treated reads (BS-Seq). BRAT-nova is very fast and accurate. On the human genome, BRAT-nova is 2\u20137 times faster than state-of-the-art aligners, while maintaining the same percentage of uniquely mapped reads and space usage. On synthetic reads, BRAT-nova is 2\u20138 times faster than state-of-the-art aligners while maintaining similar mapping accuracy, methylation call accuracy, methylation level accuracy and space efficiency.<\/jats:p>\n               <jats:p>Availability and implementation: The software is available in the public domain at http:\/\/compbio.cs.ucr.edu\/brat\/<\/jats:p>\n               <jats:p>Contact: \u00a0elenah@cs.ucr.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw226","type":"journal-article","created":{"date-parts":[[2016,4,24]],"date-time":"2016-04-24T00:17:47Z","timestamp":1461457067000},"page":"2696-2698","source":"Crossref","is-referenced-by-count":19,"title":["BRAT-nova: fast and accurate mapping of bisulfite-treated reads"],"prefix":"10.1093","volume":"32","author":[{"given":"Elena Y.","family":"Harris","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, California State University, Chico, CA 95929, USA"}]},{"given":"Rachid","family":"Ounit","sequence":"additional","affiliation":[{"name":"2 Department of Computer Science and Eng, University of California, Riverside, CA 92521, USA"}]},{"given":"Stefano","family":"Lonardi","sequence":"additional","affiliation":[{"name":"2 Department of Computer Science and Eng, University of California, Riverside, CA 92521, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,2,23]]},"reference":[{"key":"2023020112593199900_btw226-B1","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/1471-2105-11-203","article-title":"BS Seeker: precise mapping for bisulfite sequencing","volume":"11","author":"Chen","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020112593199900_btw226-B2","article-title":"Opportunistic data structures with applications","author":"Ferragina","year":"2000","journal-title":"Proceedings of IEEE Foundation of Computer Science"},{"key":"2023020112593199900_btw226-B3","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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