{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T22:05:45Z","timestamp":1788473145632,"version":"build-2803163510"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases.<\/jats:p>\n                  <jats:p>Results: To align our large (&amp;gt;80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of &amp;gt;50 in mapping speed, aligning to the human genome 550 million 2 \u00d7 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80\u201390% success rate, corroborating the high precision of the STAR mapping strategy.<\/jats:p>\n                  <jats:p>Availability and implementation: STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http:\/\/code.google.com\/p\/rna-star\/.<\/jats:p>\n                  <jats:p>Contact: \u00a0dobin@cshl.edu.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts635","type":"journal-article","created":{"date-parts":[[2012,10,26]],"date-time":"2012-10-26T20:18:50Z","timestamp":1351282730000},"page":"15-21","source":"Crossref","is-referenced-by-count":51688,"title":["STAR: ultrafast universal RNA-seq aligner"],"prefix":"10.1093","volume":"29","author":[{"given":"Alexander","family":"Dobin","sequence":"first","affiliation":[{"name":"1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA and 2Pacific Biosciences, Menlo Park, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carrie A.","family":"Davis","sequence":"additional","affiliation":[{"name":"1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA and 2Pacific Biosciences, Menlo Park, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felix","family":"Schlesinger","sequence":"additional","affiliation":[{"name":"1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA and 2Pacific Biosciences, Menlo Park, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorg","family":"Drenkow","sequence":"additional","affiliation":[{"name":"1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA and 2Pacific Biosciences, Menlo Park, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris","family":"Zaleski","sequence":"additional","affiliation":[{"name":"1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA and 2Pacific Biosciences, Menlo Park, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonali","family":"Jha","sequence":"additional","affiliation":[{"name":"1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA and 2Pacific Biosciences, Menlo Park, CA, 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