{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T14:41:45Z","timestamp":1787236905424,"version":"build-2736575974"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: NGSUtils is a suite of software tools for manipulating data common to next-generation sequencing experiments, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis.<\/jats:p>\n                  <jats:p>Availability and implementation: NGSUtils is available under a BSD license and works on Mac OS X and Linux systems. Python 2.6+ and virtualenv are required. More information and source code may be obtained from the website: http:\/\/ngsutils.org.<\/jats:p>\n                  <jats:p>Contact: \u00a0yunliu@iupui.edu<\/jats:p>\n                  <jats:p>Supplemental information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts731","type":"journal-article","created":{"date-parts":[[2013,1,12]],"date-time":"2013-01-12T20:41:16Z","timestamp":1358023276000},"page":"494-496","source":"Crossref","is-referenced-by-count":275,"title":["NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets"],"prefix":"10.1093","volume":"29","author":[{"given":"Marcus R.","family":"Breese","sequence":"first","affiliation":[{"name":"1 Center for Computational Biology and Bioinformatics, 2Center for Medical Genomics and 3Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"},{"name":"1 Center for Computational Biology and Bioinformatics, 2Center for Medical Genomics and 3Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"},{"name":"1 Center for Computational Biology and Bioinformatics, 2Center for Medical Genomics and 3Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunlong","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Center for Computational Biology and Bioinformatics, 2Center for Medical Genomics and 3Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"},{"name":"1 Center for Computational Biology and Bioinformatics, 2Center for Medical Genomics and 3Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"},{"name":"1 Center for Computational Biology and Bioinformatics, 2Center for Medical Genomics and 3Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,1,12]]},"reference":[{"key":"2023012810251014900_bts731-B1","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","article-title":"The Sanger FASTQ file format for sequences with quality scores, and the Solexa\/Illumina FASTQ variants","volume":"38","author":"Cock","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012810251014900_bts731-B2","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810251014900_bts731-B3","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023012810251014900_bts731-B4","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":"2023012810251014900_bts731-B5","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. 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Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/4\/494\/48895499\/bioinformatics_29_4_494.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/4\/494\/48895499\/bioinformatics_29_4_494.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T06:54:15Z","timestamp":1674888855000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/4\/494\/200293"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,12]]},"references-count":9,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2013,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts731","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,2,15]]},"published":{"date-parts":[[2013,1,12]]}}}