{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T07:59:47Z","timestamp":1775807987993,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1018,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation:\u2003Using high-throughput sequencing, researchers are now generating hundreds of whole-genome assays to measure various features such as transcription factor binding, histone marks, DNA methylation or RNA transcription. Displaying so much data generally leads to a confusing accumulation of plots. We describe here a multithreaded library that computes statistics on large numbers of datasets (Wiggle, BigWig, Bed, BigBed and BAM), generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions.<\/jats:p>\n               <jats:p>Availability and Implementation: The code is freely available under Apache 2.0 license at www.github.com\/Ensembl\/Wiggletools<\/jats:p>\n               <jats:p>Contact: \u00a0zerbino@ebi.ac.uk or flicek@ebi.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt737","type":"journal-article","created":{"date-parts":[[2013,12,21]],"date-time":"2013-12-21T03:17:47Z","timestamp":1387595867000},"page":"1008-1009","source":"Crossref","is-referenced-by-count":206,"title":["WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis"],"prefix":"10.1093","volume":"30","author":[{"given":"Daniel R.","family":"Zerbino","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Nathan","family":"Johnson","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Thomas","family":"Juettemann","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Steven P.","family":"Wilder","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Paul","family":"Flicek","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]}],"member":"286","published-online":{"date-parts":[[2013,12,19]]},"reference":[{"key":"2023012710450867400_btt737-B1","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1038\/nbt.2153","article-title":"BLUEPRINT to decode the epigenetic signature written in blood","volume":"30","author":"Adams","year":"2012","journal-title":"Nat. Biotech."},{"key":"2023012710450867400_btt737-B2","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1038\/nbt1010-1045","article-title":"The NIH roadmap epigenomics mapping consortium","volume":"28","author":"Bernstein","year":"2010","journal-title":"Nat. Biotech."},{"key":"2023012710450867400_btt737-B3","doi-asserted-by":"crossref","first-page":"D48","DOI":"10.1093\/nar\/gks1236","article-title":"Ensembl 2013","volume":"41","author":"Flicek","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012710450867400_btt737-B4","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1093\/bioinformatics\/btq351","article-title":"BigWig and BigBed: enabling browsing of large distributed datasets","volume":"26","author":"Kent","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012710450867400_btt737-B5","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":"2023012710450867400_btt737-B6","doi-asserted-by":"crossref","first-page":"D64","DOI":"10.1093\/nar\/gks1048","article-title":"The UCSC genome browser database: extensions and updates 2013","volume":"41","author":"Meyer","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012710450867400_btt737-B7","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"},{"key":"2023012710450867400_btt737-B8","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2013"},{"key":"2023012710450867400_btt737-B9","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"The ENCODE Project Consortium","year":"2012","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/7\/1008\/48921616\/bioinformatics_30_7_1008.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/7\/1008\/48921616\/bioinformatics_30_7_1008.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:13:02Z","timestamp":1674817982000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/7\/1008\/235372"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,12,19]]},"references-count":9,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2014,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt737","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,4,1]]},"published":{"date-parts":[[2013,12,19]]}}}