{"id":"https://openalex.org/W2912500497","doi":"https://doi.org/10.1093/bioinformatics/btm542","title":"Assembly reconciliation","display_name":"Assembly reconciliation","publication_year":2007,"publication_date":"2007-12-05","ids":{"openalex":"https://openalex.org/W2912500497","doi":"https://doi.org/10.1093/bioinformatics/btm542","mag":"2912500497","pmid":"https://pubmed.ncbi.nlm.nih.gov/18057021"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm542","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm542","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/1/42/537020/btm542.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/1/42/537020/btm542.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056359638","display_name":"Aleksey V. Zimin","orcid":"https://orcid.org/0000-0001-5091-3092"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Aleksey V. Zimin","raw_affiliation_strings":["1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031528898","display_name":"Douglas R. Smith","orcid":"https://orcid.org/0000-0002-7194-5787"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas R. Smith","raw_affiliation_strings":["1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028284504","display_name":"Granger Sutton","orcid":"https://orcid.org/0000-0001-7498-8048"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Granger Sutton","raw_affiliation_strings":["1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022360238","display_name":"James A. Yorke","orcid":"https://orcid.org/0000-0002-9599-0136"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James A. Yorke","raw_affiliation_strings":["1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 IPST, University of Maryland, College Park, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5056359638"],"corresponding_institution_ids":["https://openalex.org/I66946132"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":1.3845,"has_fulltext":true,"cited_by_count":75,"citation_normalized_percentile":{"value":0.80405275,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"24","issue":"1","first_page":"42","last_page":"45"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8917999863624573,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8917999863624573,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.07169999927282333,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.003599999938160181,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5619372725486755},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.33937954902648926}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5619372725486755},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.33937954902648926}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm542","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm542","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/1/42/537020/btm542.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18057021","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18057021","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm542","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm542","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/1/42/537020/btm542.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8124727942","display_name":null,"funder_award_id":"1R01HG0294501","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2912500497.pdf","grobid_xml":"https://content.openalex.org/works/W2912500497.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1635391495","https://openalex.org/W1992950355","https://openalex.org/W2008235493","https://openalex.org/W2010454899","https://openalex.org/W2032379826","https://openalex.org/W2095685450","https://openalex.org/W2107282968","https://openalex.org/W2141217788","https://openalex.org/W2144662851","https://openalex.org/W2152331922","https://openalex.org/W2161668137"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"MOTIVATION:":[0],"Many":[1],"genomes":[2],"are":[3,131],"sequenced":[4],"by":[5],"a":[6,53,143],"collaboration":[7,119],"of":[8,95,114,146],"several":[9],"centers,":[10],"and":[11,37,123,150],"then":[12,25],"each":[13],"center":[14],"produces":[15],"an":[16],"assembly":[17,21,29,58,145,152],"using":[18,81],"their":[19],"own":[20],"software.":[22],"The":[23,124,160],"collaborators":[24],"pick":[26],"the":[27,35,38,42,78,96,101,106,133],"draft":[28,63,69,85],"that":[30,55,60],"they":[31],"judge":[32],"to":[33],"be":[34],"best":[36],"information":[39],"contained":[40],"in":[41,91,118],"other":[43],"assemblies":[44,98,113,130,136],"is":[45,153,163],"usually":[46],"not":[47],"used.":[48],"METHODS:":[49],"We":[50,140],"have":[51],"developed":[52],"technique":[54],"we":[56,110],"call":[57],"reconciliation":[59,161],"can":[61],"merge":[62],"genome":[64],"assemblies.":[65,86],"It":[66,87],"takes":[67],"one":[68,94],"assembly,":[70],"detects":[71],"apparent":[72],"errors,":[73],"and,":[74],"when":[75],"possible,":[76],"patches":[77],"problem":[79],"areas":[80],"pieces":[82],"from":[83,155,167],"alternative":[84,97],"also":[88,141],"closes":[89],"gaps":[90],"places":[92],"where":[93],"has":[99],"spanned":[100],"gap":[102],"correctly.":[103],"RESULTS:":[104],"Using":[105],"Assembly":[107],"Reconciliation":[108],"technique,":[109],"produced":[111,142],"reconciled":[112,144],"six":[115],"Drosophila":[116],"species":[117],"with":[120],"Agencourt":[121],"Bioscience":[122],"J.":[125],"Craig":[126],"Venter":[127],"Institute.":[128],"These":[129],"now":[132],"official":[134],"(CAF1)":[135],"used":[137],"for":[138,165],"analysis.":[139],"Rhesus":[147],"Macaque":[148],"genome,":[149],"this":[151],"available":[154,164],"our":[156],"website":[157],"http://www.genome.umd.edu.":[158],"AVAILABILITY:":[159],"software":[162],"download":[166],"http://www.genome.umd.edu/software.htm":[168]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":5}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
