{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,8]],"date-time":"2025-04-08T05:23:20Z","timestamp":1744089800853,"version":"3.37.3"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"24","funder":[{"name":"NICTA Victorian Research Laboratory"},{"DOI":"10.13039\/100015539","name":"Australian Government","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100015539","id-type":"DOI","asserted-by":"crossref"}]},{"name":"the Department of Broadband, Communications and the Digital Economy and the Australian Research Council"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,15]]},"abstract":"<jats:p>Motivation: Next generation sequencing machines produce vast amounts of genomic data. For the data to be useful, it is essential that it can be stored and manipulated efficiently. This work responds to the combined challenge of compressing genomic data, while providing fast access to regions of interest, without necessitating decompression of whole files.<\/jats:p>\n               <jats:p>Results: We describe CSAM (Compressed SAM format), a compression approach offering lossless and lossy compression for SAM files. The structures and techniques proposed are suitable for representing SAM files, as well as supporting fast access to the compressed information. They generate more compact lossless representations than BAM, which is currently the preferred lossless compressed SAM-equivalent format; and are self-contained, that is, they do not depend on any external resources to compress or decompress SAM files.<\/jats:p>\n               <jats:p>Availability and Implementation: An implementation is available at https:\/\/github.com\/rcanovas\/libCSAM.<\/jats:p>\n               <jats:p>Contact: \u00a0canovas-ba@lirmm.fr<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw543","type":"journal-article","created":{"date-parts":[[2016,8,19]],"date-time":"2016-08-19T01:19:13Z","timestamp":1471569553000},"page":"3709-3716","source":"Crossref","is-referenced-by-count":12,"title":["CSAM: Compressed SAM format"],"prefix":"10.1093","volume":"32","author":[{"given":"Rodrigo","family":"C\u00e1novas","sequence":"first","affiliation":[{"name":"1L.I.R.M.M. and Institut Biologie Computationnelle, Universit\u00e9 de Montpellier, Montpellier Cedex 5, CNRS F-34392, France"},{"name":"2Department of Computing and Information Systems, The University of Melbourne, Victoria 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alistair","family":"Moffat","sequence":"additional","affiliation":[{"name":"2Department of Computing and Information Systems, The University of Melbourne, Victoria 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew","family":"Turpin","sequence":"additional","affiliation":[{"name":"2Department of Computing and Information Systems, The University of Melbourne, Victoria 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,8,18]]},"reference":[{"key":"2023020114084607400_btw543-B1","article-title":"An evaluation framework for lossy compression of genome sequencing quality values","author":"Alberti","year":"2016","journal-title":"Data Compression Conference (DCC)"},{"key":"2023020114084607400_btw543-B2","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq - A python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020114084607400_btw543-B3","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.nbt.2008.12.009","article-title":"Next-generation DNA sequencing techniques","volume":"25","author":"Ansorge","year":"2009","journal-title":"New Biotechnol"},{"key":"2023020114084607400_btw543-B4","doi-asserted-by":"crossref","first-page":"2818","DOI":"10.1093\/bioinformatics\/btu390","article-title":"The Scramble conversion tool","volume":"30","author":"Bonfield","year":"2014","journal-title":"Bioinformatics"},{"year":"2015","author":"C\u00e1novas","key":"2023020114084607400_btw543-B5"},{"first-page":"51","year":"2013","author":"C\u00e1novas","key":"2023020114084607400_btw543-B6"},{"key":"2023020114084607400_btw543-B7","doi-asserted-by":"crossref","first-page":"2130","DOI":"10.1093\/bioinformatics\/btu183","article-title":"Lossy compression of quality scores in genomic data","volume":"30","author":"C\u00e1novas","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020114084607400_btw543-B8","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/scientificamerican0106-46","article-title":"Genomes for all","volume":"294","author":"Church","year":"2006","journal-title":"Sci. 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