{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T12:51:31Z","timestamp":1783947091141,"version":"3.55.0"},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2014,5,7]],"date-time":"2014-05-07T00:00:00Z","timestamp":1399420800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,1]]},"abstract":"<jats:p>Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times.<\/jats:p>\n               <jats:p>Results: We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and\/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results.<\/jats:p>\n               <jats:p>Availability and implementation: SAMBLASTER is open-source C++ code and freely available for download from https:\/\/github.com\/GregoryFaust\/samblaster.<\/jats:p>\n               <jats:p>Contact: \u00a0imh4y@virginia.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu314","type":"journal-article","created":{"date-parts":[[2014,5,9]],"date-time":"2014-05-09T04:37:58Z","timestamp":1399610278000},"page":"2503-2505","source":"Crossref","is-referenced-by-count":910,"title":["<i>SAMBLASTER<\/i>: fast duplicate marking and structural variant read extraction"],"prefix":"10.1093","volume":"30","author":[{"given":"Gregory G.","family":"Faust","sequence":"first","affiliation":[{"name":"1 \u00a01Department of Biochemistry and Molecular Genetics and 2Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ira M.","family":"Hall","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Biochemistry and Molecular Genetics and 2Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,5,7]]},"reference":[{"key":"2023012711525809100_btu314-B1","doi-asserted-by":"crossref","first-page":"2417","DOI":"10.1093\/bioinformatics\/bts456","article-title":"YAHA: fast and flexible long-read alignment with optimal breakpoint detection","volume":"28","author":"Faust","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012711525809100_btu314-B2","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012711525809100_btu314-B3","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1101\/gr.102970.109","article-title":"Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome","volume":"20","author":"Quinlan","year":"2010","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/17\/2503\/48927353\/bioinformatics_30_17_2503.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/17\/2503\/48927353\/bioinformatics_30_17_2503.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:11:22Z","timestamp":1674821482000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/17\/2503\/2748175"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,7]]},"references-count":3,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2014,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu314","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,5,7]]}}}