{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T11:52:05Z","timestamp":1775303525167,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3224,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Many genomes are sequenced by a collaboration of several centers, and then each center produces an assembly using their own assembly software. The collaborators then pick the draft assembly that they judge to be the best and the information contained in the other assemblies is usually not used.<\/jats:p>\n               <jats:p>Methods: We have developed a technique that we call assembly reconciliation that can merge draft genome assemblies. It takes one draft assembly, detects apparent errors, and, when possible, patches the problem areas using pieces from alternative draft assemblies. It also closes gaps in places where one of the alternative assemblies has spanned the gap correctly.<\/jats:p>\n               <jats:p>Results: Using the Assembly Reconciliation technique, we produced reconciled assemblies of six Drosophila species in collaboration with Agencourt Bioscience and The J. Craig Venter Institute. These assemblies are now the official (CAF1) assemblies used for analysis. We also produced a reconciled assembly of Rhesus Macaque genome, and this assembly is available from our website http:\/\/www.genome.umd.edu.<\/jats:p>\n               <jats:p>Availability: The reconciliation software is available for download from http:\/\/www.genome.umd.edu\/software.htm<\/jats:p>\n               <jats:p>Contact: \u00a0alekseyz@ipst.umd.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm542","type":"journal-article","created":{"date-parts":[[2007,12,6]],"date-time":"2007-12-06T01:14:34Z","timestamp":1196903674000},"page":"42-45","source":"Crossref","is-referenced-by-count":62,"title":["Assembly reconciliation"],"prefix":"10.1093","volume":"24","author":[{"given":"Aleksey V.","family":"Zimin","sequence":"first","affiliation":[{"name":"1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Douglas R.","family":"Smith","sequence":"additional","affiliation":[{"name":"1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Granger","family":"Sutton","sequence":"additional","affiliation":[{"name":"1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James A.","family":"Yorke","sequence":"additional","affiliation":[{"name":"1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,12,5]]},"reference":[{"key":"2023020209443029700_B1","first-page":"177","article-title":"ARACHNE: a whole-genome shotgun assembler","volume":"12","author":"Batzoglou","year":"2002","journal-title":"Genome Res"},{"key":"2023020209443029700_B2","doi-asserted-by":"crossref","first-page":"2369","DOI":"10.1093\/nar\/27.11.2369","article-title":"Alignment of whole genomes","volume":"27","author":"Delcher","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2023020209443029700_B3","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1093\/nar\/30.11.2478","article-title":"Fast algorithms for large-scale genome alignment and comparison","volume":"30","author":"Delcher","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2023020209443029700_B4","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1089\/cmb.2005.12.497","article-title":"A tool for analyzing mate pairs in assemblies (TAMPA)","volume":"12","author":"Dew","year":"2005","journal-title":"J. Comput. Biol"},{"key":"2023020209443029700_B5","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1101\/gr.828403","article-title":"Whole-genome sequence assembly for mammalian genomes: Arachne 2","volume":"13","author":"Jaffe","year":"2003","journal-title":"Genome Res"},{"key":"2023020209443029700_B6","doi-asserted-by":"crossref","first-page":"2164","DOI":"10.1101\/gr.1390403","article-title":"PCAP: a whole-genome assembly program","volume":"13","author":"Huang","year":"2003","journal-title":"Genome Res"},{"key":"2023020209443029700_B7","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2003","journal-title":"Genome Biol"},{"key":"2023020209443029700_B8","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1101\/gr.731003","article-title":"The phusion assembler","volume":"13","author":"Mullikin","year":"2002","journal-title":"Genome Res"},{"key":"2023020209443029700_B9","doi-asserted-by":"crossref","first-page":"2196","DOI":"10.1126\/science.287.5461.2196","article-title":"A whole-genome assembly of Drosophila","volume":"287","author":"Myers","year":"2000","journal-title":"Science"},{"key":"2023020209443029700_B10","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1089\/cmb.2004.11.734","article-title":"A preprocessor for shotgun assembly of large genomes","volume":"11","author":"Roberts","year":"2004","journal-title":"J. Comput. Biol"},{"key":"2023020209443029700_B11","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1016\/0022-2836(82)90546-0","article-title":"Nucleotide sequence of bacteriophage lambda DNA","volume":"162","author":"Sanger","year":"1982","journal-title":"J. Mol. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/1\/42\/49044105\/bioinformatics_24_1_42.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/1\/42\/49044105\/bioinformatics_24_1_42.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T09:59:25Z","timestamp":1675331965000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/1\/42\/205726"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,12,5]]},"references-count":11,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm542","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,1,1]]},"published":{"date-parts":[[2007,12,5]]}}}