{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T00:59:56Z","timestamp":1778029196703,"version":"3.51.4"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2016,10,28]],"date-time":"2016-10-28T00:00:00Z","timestamp":1477612800000},"content-version":"vor","delay-in-days":204,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: For most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly. However, the local accuracy of an assembly remains difficult to assess and improve. The gEVAL browser allows the user to interrogate an assembly in any region of the genome by comparing it to different datasets and evaluating the concordance. These analyses include: a wide variety of sequence alignments, comparative analyses of multiple genome assemblies, and consistency with optical and other physical maps. gEVAL highlights allelic variations, regions of low complexity, abnormal coverage, and potential sequence and assembly errors, and offers strategies for improvement. Although gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including from Ensembl or TrackHub sources. We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly.<\/jats:p>\n                  <jats:p>Availability and Implementation: Web Browser: http:\/\/geval.sanger.ac.uk, Plugin: http:\/\/wchow.github.io\/wtsi-geval-plugin.<\/jats:p>\n                  <jats:p>Contact: \u00a0kj2@sanger.ac.uk<\/jats:p>\n                  <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw159","type":"journal-article","created":{"date-parts":[[2016,4,8]],"date-time":"2016-04-08T14:25:27Z","timestamp":1460125527000},"page":"2508-2510","source":"Crossref","is-referenced-by-count":401,"title":["gEVAL\u2009\u2014\u2009a web-based browser for evaluating genome assemblies"],"prefix":"10.1093","volume":"32","author":[{"given":"William","family":"Chow","sequence":"first","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kim","family":"Brugger","sequence":"additional","affiliation":[{"name":"2 East Anglian Medical Genetics Centre, Cambridge University Hospitals, NHS Foundation Trust, Cambridge CB2 0QQ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mario","family":"Caccamo","sequence":"additional","affiliation":[{"name":"3 National Institute of Agricultural Botany, Cambridge CB3 0LE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian","family":"Sealy","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Torrance","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kerstin","family":"Howe","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,4,7]]},"reference":[{"key":"2023020112532905400_btw159-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1007\/s00335-015-9579-6","article-title":"The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes","volume":"26","author":"Adams","year":"2015","journal-title":"Mamm. Genome"},{"key":"2023020112532905400_btw159-B2","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1101\/gr.1860604","article-title":"An overview of Ensembl","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res"},{"key":"2023020112532905400_btw159-B3","doi-asserted-by":"crossref","first-page":"e1001091","DOI":"10.1371\/journal.pbio.1001091","article-title":"Modernizing reference genome assemblies","volume":"9","author":"Church","year":"2011","journal-title":"Plos Biol"},{"key":"2023020112532905400_btw159-B4","doi-asserted-by":"crossref","first-page":"D662","DOI":"10.1093\/nar\/gku1010","article-title":"Ensembl 2015","volume":"43","author":"Cunningham","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020112532905400_btw159-B5","doi-asserted-by":"crossref","first-page":"e1003998","DOI":"10.1371\/journal.pcbi.1003998","article-title":"Extensive error in the number of genes inferred from draft genome assemblies","volume":"10","author":"Denton","year":"2014","journal-title":"Plos Comput. Biol"},{"key":"2023020112532905400_btw159-B6","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1038\/nature11622","article-title":"Analyses of pig genomes provide insight into porcine demography and evolution","volume":"491","author":"Groenen","year":"2012","journal-title":"Nature"},{"key":"2023020112532905400_btw159-B7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00251-007-0262-2","article-title":"Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project","volume":"60","author":"Horton","year":"2008","journal-title":"Immunogenetics"},{"key":"2023020112532905400_btw159-B8","doi-asserted-by":"crossref","first-page":"10.","DOI":"10.1186\/s13742-015-0052-y","article-title":"Using optical mapping data for the improvement of vertebrate genome assemblies","volume":"4","author":"Howe","year":"2015","journal-title":"Gigascience"},{"key":"2023020112532905400_btw159-B9","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1038\/nature03001","article-title":"Finishing the euchromatic sequence of the human genome","volume":"431","author":"International Human Genome Sequencing Consortium","year":"2004","journal-title":"Nature"},{"key":"2023020112532905400_btw159-B10","first-page":"403","article-title":"Genome-wide structural variation detection by genome mapping on nanochannel arrays","volume":"26","author":"Mak","year":"2015","journal-title":"Genetics"},{"key":"2023020112532905400_btw159-B11","doi-asserted-by":"crossref","first-page":"D670","DOI":"10.1093\/nar\/gku1177","article-title":"The UCSC Genome Browser database: 2015 update","volume":"43","author":"Rosenbloom","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020112532905400_btw159-B12","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1159\/000430927","article-title":"Third report on chicken genes and chromosomes 2015","volume":"145","author":"Schmid","year":"2015","journal-title":"Cytogenet. Genome Res"},{"key":"2023020112532905400_btw159-B13","doi-asserted-by":"crossref","first-page":"10848","DOI":"10.1073\/pnas.0914638107","article-title":"High-resolution human genome structure by single molecule analysis","volume":"107","author":"Teague","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020112532905400_btw159-B14","doi-asserted-by":"crossref","first-page":"338","DOI":"10.3389\/fgene.2015.00338","article-title":"Identification of low-confidence regions in the pig reference genome (Sscrofa10.2)","volume":"6","author":"Warr","year":"2015","journal-title":"Front. Genet"},{"key":"2023020112532905400_btw159-B15","article-title":"Extensive sequencing of seven human genomes to characterize benchmark reference materials","author":"Zook","year":"2015","journal-title":"bioRxiv"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/16\/2508\/49020354\/bioinformatics_32_16_2508.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/16\/2508\/49020354\/bioinformatics_32_16_2508.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T17:52:57Z","timestamp":1675273977000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/16\/2508\/1743061"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,4,7]]},"references-count":15,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2016,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw159","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/038638","asserted-by":"object"}]},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,8,15]]},"published":{"date-parts":[[2016,4,7]]}}}