{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T05:48:29Z","timestamp":1768974509123,"version":"3.49.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Accurately mapping RNA-Seq reads to the reference genome is a critical step for performing downstream analysis such as transcript assembly, isoform detection and quantification. Many tools have been developed; however, given the huge size of the next generation sequencing datasets and the complexity of the transcriptome, RNA-Seq read mapping remains a challenge with the ever-increasing amount of data. We develop Omicsoft sequence aligner (OSA), a fast and accurate alignment tool for RNA-Seq data. Benchmarked with existing methods, OSA improves mapping speed 4\u201310-fold with better sensitivity and less false positives.<\/jats:p>\n               <jats:p>Availability: OSA can be downloaded from http:\/\/omicsoft.com\/osa. It is free to academic users. OSA has been tested extensively on Linux, Mac OS X and Windows platforms.<\/jats:p>\n               <jats:p>Contact: \u00a0john.hu@omicsoft.com; jhu7@ncsu.edu; jack.liu@omicsoft.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts294","type":"journal-article","created":{"date-parts":[[2012,5,17]],"date-time":"2012-05-17T15:46:05Z","timestamp":1337269565000},"page":"1933-1934","source":"Crossref","is-referenced-by-count":116,"title":["OSA: a fast and accurate alignment tool for RNA-Seq"],"prefix":"10.1093","volume":"28","author":[{"given":"Jun","family":"Hu","sequence":"first","affiliation":[{"name":"1 Division of Bioinformatics, Omicsoft Inc., 164 Quade Drive, Cary, NC 27513, USA, 2Bioinformatics Research Center, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA and 3Genome Analysis Unit, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA"},{"name":"1 Division of Bioinformatics, Omicsoft Inc., 164 Quade Drive, Cary, NC 27513, USA, 2Bioinformatics Research Center, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA and 3Genome Analysis Unit, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huanying","family":"Ge","sequence":"additional","affiliation":[{"name":"1 Division of Bioinformatics, Omicsoft Inc., 164 Quade Drive, Cary, NC 27513, USA, 2Bioinformatics Research Center, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA and 3Genome Analysis Unit, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matt","family":"Newman","sequence":"additional","affiliation":[{"name":"1 Division of Bioinformatics, Omicsoft Inc., 164 Quade Drive, Cary, NC 27513, USA, 2Bioinformatics Research Center, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA and 3Genome Analysis Unit, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kejun","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Division of Bioinformatics, Omicsoft Inc., 164 Quade Drive, Cary, NC 27513, USA, 2Bioinformatics Research Center, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA and 3Genome Analysis Unit, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,4,11]]},"reference":[{"key":"2023012512434792400_B1","doi-asserted-by":"crossref","first-page":"4570","DOI":"10.1093\/nar\/gkq211","article-title":"Detection of splice junctions from paired-end RNA-seq data by SpliceMap","volume":"38","author":"Au","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512434792400_B2","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1093\/nar\/29.1.255","article-title":"SpliceDB: database of canonical and non-canonical mammalian splice sites","volume":"29","author":"Burset","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023012512434792400_B3","doi-asserted-by":"crossref","first-page":"e42","DOI":"10.1093\/nar\/gkr1248","article-title":"RNASEQR\u2014a streamlined and accurate RNA-seq sequence analysis program","volume":"40","author":"Chen","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023012512434792400_B4","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1471-2105-11-38","article-title":"SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read","volume":"11","author":"Falgueras","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012512434792400_B5","doi-asserted-by":"crossref","first-page":"2518","DOI":"10.1093\/bioinformatics\/btr427","article-title":"Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)","volume":"27","author":"Grant","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512434792400_B6","doi-asserted-by":"crossref","first-page":"46","DOI":"10.3389\/fgene.2011.00046","article-title":"SOAPsplice: genome-wide ab initio detection of splice junctions from RNA-Seq data","volume":"2","author":"Huang","year":"2011","journal-title":"Front. 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