{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T08:08:17Z","timestamp":1775981297575,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,12,27]],"date-time":"2020-12-27T00:00:00Z","timestamp":1609027200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG010040"],"award-info":[{"award-number":["R01HG010040"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We present bedtk, a new toolkit for manipulating genomic intervals in the BED format. It supports sorting, merging, intersection, subtraction and the calculation of the breadth of coverage. Bedtk uses implicit interval tree, a data structure for fast interval overlap queries. It is several to tens of times faster than existing tools and tends to use less memory.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code is available at https:\/\/github.com\/lh3\/bedtk.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa827","type":"journal-article","created":{"date-parts":[[2020,9,9]],"date-time":"2020-09-09T15:27:03Z","timestamp":1599665223000},"page":"1315-1316","source":"Crossref","is-referenced-by-count":13,"title":["Bedtk: finding interval overlap with implicit interval tree"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4874-2874","authenticated-orcid":false,"given":"Heng","family":"Li","sequence":"first","affiliation":[{"name":"Department of Data Science, Dana-Faber Cancer Institute , Boston, MA 02215, USA"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02215, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7884-5973","authenticated-orcid":false,"given":"Jiazhen","family":"Rong","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02215, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,12,27]]},"reference":[{"key":"2023051705212257800_btaa827-B1","doi-asserted-by":"crossref","first-page":"1386","DOI":"10.1093\/bioinformatics\/btl647","article-title":"Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases","volume":"23","author":"Alekseyenko","year":"2007","journal-title":"Bioinformatics"},{"key":"2023051705212257800_btaa827-B2","first-page":"39","author":"Brodal","year":"2002"},{"key":"2023051705212257800_btaa827-B3","doi-asserted-by":"crossref","first-page":"4907","DOI":"10.1093\/bioinformatics\/btz407","article-title":"Augmented Interval List: a novel data structure for efficient genomic interval search","volume":"35","author":"Feng","year":"2019","journal-title":"Bioinformatics"},{"key":"2023051705212257800_btaa827-B4","author":"Khuong","year":"2017"},{"key":"2023051705212257800_btaa827-B5","doi-asserted-by":"crossref","first-page":"1919","DOI":"10.1093\/bioinformatics\/bts277","article-title":"BEDOPS: high-performance genomic feature operations","volume":"28","author":"Neph","year":"2012","journal-title":"Bioinformatics"},{"key":"2023051705212257800_btaa827-B6","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":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa827\/35175657\/btaa827.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/9\/1315\/50359653\/btaa827.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/9\/1315\/50359653\/btaa827.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T01:22:17Z","timestamp":1684286537000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/9\/1315\/5910546"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,12,27]]},"references-count":6,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2021,6,9]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa827","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.07.07.190744","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":[[2021,5,1]]},"published":{"date-parts":[[2020,12,27]]}}}