{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:49Z","timestamp":1772138089644,"version":"3.50.1"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2018,4,30]],"date-time":"2018-04-30T00:00:00Z","timestamp":1525046400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"US National Human Genome Research Institute","award":["NIH R01HG006693"],"award-info":[{"award-number":["NIH R01HG006693"]}]},{"name":"US National Human Genome Research Institute","award":["NIH R01HG009141"],"award-info":[{"award-number":["NIH R01HG009141"]}]},{"DOI":"10.13039\/100000057","name":"US National Institute of General Medical Sciences","doi-asserted-by":"crossref","award":["NIH R01GM124355"],"award-info":[{"award-number":["NIH R01GM124355"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000054","name":"US National Cancer Institute","doi-asserted-by":"crossref","award":["NIH U24CA209999"],"award-info":[{"award-number":["NIH U24CA209999"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,10,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Extracting biological insight from genomic data inevitably requires custom software. In many cases, this is accomplished with scripting languages, owing to their accessibility and brevity. Unfortunately, the ease of scripting languages typically comes at a substantial performance cost that is especially acute with the scale of modern genomics datasets.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n We present hts-nim, a high-performance library written in the Nim programming language that provides a simple, scripting-like syntax without sacrificing performance.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n hts-nim is available at https:\/\/github.com\/brentp\/hts-nim and the example tools are at https:\/\/github.com\/brentp\/hts-nim-tools both under the MIT license.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty358","type":"journal-article","created":{"date-parts":[[2018,4,27]],"date-time":"2018-04-27T15:10:38Z","timestamp":1524841838000},"page":"3387-3389","source":"Crossref","is-referenced-by-count":28,"title":["hts-nim: scripting high-performance genomic analyses"],"prefix":"10.1093","volume":"34","author":[{"given":"Brent S","family":"Pedersen","sequence":"first","affiliation":[{"name":"Department of Human Genetics, Department of Biomedical Informatics, and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA"}]},{"given":"Aaron R","family":"Quinlan","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Department of Biomedical Informatics, and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,4,30]]},"reference":[{"key":"2023012712493544800_bty358-B1","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":"2023012712493544800_bty358-B2","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nature19057","article-title":"Analysis of protein-coding genetic variation in 60, 706 humans","volume":"536","author":"Lek","year":"2016","journal-title":"Nature"},{"key":"2023012712493544800_bty358-B3","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":"2023012712493544800_bty358-B4","first-page":"867","author":"Pedersen","year":"2017"},{"key":"2023012712493544800_bty358-B5","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"Bedtools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/19\/3387\/48919679\/bioinformatics_34_19_3387.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/19\/3387\/48919679\/bioinformatics_34_19_3387.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T07:50:00Z","timestamp":1674805800000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/19\/3387\/4990493"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,4,30]]},"references-count":5,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2018,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty358","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/261735","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,10,1]]},"published":{"date-parts":[[2018,4,30]]}}}