{"id":"https://openalex.org/W4310416257","doi":"https://doi.org/10.1093/bioinformatics/btac743","title":"Unbiased pangenome graphs","display_name":"Unbiased pangenome graphs","publication_year":2022,"publication_date":"2022-11-30","ids":{"openalex":"https://openalex.org/W4310416257","doi":"https://doi.org/10.1093/bioinformatics/btac743","pmid":"https://pubmed.ncbi.nlm.nih.gov/36448683"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac743","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac743","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac743/48448986/btac743.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","license_id":"https://openalex.org/licenses/cc-by","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/39/1/btac743/48448986/btac743.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008992371","display_name":"Erik Garrison","orcid":"https://orcid.org/0000-0003-3821-631X"},"institutions":[{"id":"https://openalex.org/I160606119","display_name":"University of Tennessee Health Science Center","ror":"https://ror.org/0011qv509","country_code":"US","type":"education","lineage":["https://openalex.org/I160606119"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Erik Garrison","raw_affiliation_strings":["Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, USA"],"raw_orcid":"https://orcid.org/0000-0003-3821-631X","affiliations":[{"raw_affiliation_string":"Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, USA","institution_ids":["https://openalex.org/I160606119"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028113588","display_name":"Andrea Guarracino","orcid":"https://orcid.org/0000-0001-9744-131X"},"institutions":[{"id":"https://openalex.org/I4210115812","display_name":"Human Technopole","ror":"https://ror.org/029gmnc79","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210115812"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Guarracino","raw_affiliation_strings":["Genomics Research Centre, Human Technopole , Viale Rita Levi-Montalcini 1 , Milan 20157, Italy"],"raw_orcid":"https://orcid.org/0000-0001-9744-131X","affiliations":[{"raw_affiliation_string":"Genomics Research Centre, Human Technopole , Viale Rita Levi-Montalcini 1 , Milan 20157, Italy","institution_ids":["https://openalex.org/I4210115812"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5008992371"],"corresponding_institution_ids":["https://openalex.org/I160606119"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.5077,"has_fulltext":true,"cited_by_count":88,"citation_normalized_percentile":{"value":0.98027793,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8888999819755554,"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":0.8888999819755554,"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":0.08089999854564667,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.004900000058114529,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.6569805145263672},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5285037159919739},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5102348327636719},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5091151595115662},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4607006907463074},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4204178750514984},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4120137095451355},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32948464155197144},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.25466567277908325},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1694757044315338},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15701666474342346},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09649023413658142}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6569805145263672},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5285037159919739},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5102348327636719},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5091151595115662},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4607006907463074},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4204178750514984},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4120137095451355},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32948464155197144},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.25466567277908325},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1694757044315338},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15701666474342346},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09649023413658142}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac743","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac743","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac743/48448986/btac743.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36448683","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36448683","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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9805579","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9805579","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac743","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac743","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac743/48448986/btac743.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1538685144","display_name":null,"funder_award_id":"NIDA U01DA047638","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G3263214147","display_name":null,"funder_award_id":"U01DA047638","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G373495704","display_name":"System genetics of menthol and nicotine addiction","funder_award_id":"5u01da047638-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4252662975","display_name":null,"funder_award_id":"2118709","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7564846446","display_name":"Collaborative Research: PPoSS: LARGE: Panorama: Integrated Rack-Scale Acceleration for Computational Pangenomics","funder_award_id":"2118709","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"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/F4320334350","display_name":"High Performance Research Computing, Texas A and M University","ror":null},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4310416257.pdf","grobid_xml":"https://content.openalex.org/works/W4310416257.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1492127831","https://openalex.org/W1962019683","https://openalex.org/W2010894431","https://openalex.org/W2055615325","https://openalex.org/W2142113273","https://openalex.org/W2254458779","https://openalex.org/W2509995029","https://openalex.org/W2547528004","https://openalex.org/W2606086658","https://openalex.org/W2789843538","https://openalex.org/W2888300707","https://openalex.org/W2892689606","https://openalex.org/W2909021353","https://openalex.org/W2952366981","https://openalex.org/W2963158913","https://openalex.org/W2988098904","https://openalex.org/W3005228641","https://openalex.org/W3007365321","https://openalex.org/W3086678357","https://openalex.org/W3088755962","https://openalex.org/W3092652421","https://openalex.org/W3100651612","https://openalex.org/W3106484143","https://openalex.org/W3131616027","https://openalex.org/W3159728495","https://openalex.org/W3183022517","https://openalex.org/W4255836900","https://openalex.org/W4280583823","https://openalex.org/W6629495972","https://openalex.org/W6691736922"],"related_works":["https://openalex.org/W2117798581","https://openalex.org/W4309247532","https://openalex.org/W3096946169","https://openalex.org/W2113128227","https://openalex.org/W2144610372","https://openalex.org/W4312114021","https://openalex.org/W4311938462","https://openalex.org/W2121840477","https://openalex.org/W2515936044","https://openalex.org/W3123068371"],"abstract_inverted_index":{"MOTIVATION:":[0],"Pangenome":[1],"variation":[2,20,91,117,161],"graphs":[3,67,205],"model":[4,53],"the":[5,85,105,116,125,141,152,182,219],"mutual":[6],"alignment":[7,106],"of":[8,10,15,47,96,124],"collections":[9],"DNA":[11,133],"sequences.":[12],"A":[13,60],"set":[14,95,107],"pairwise":[16],"alignments":[17,99,126],"implies":[18],"a":[19,31,41,44,50,56,73,90,94,136,159],"graph,":[21,118,148,157],"but":[22],"there":[23],"are":[24,228],"no":[25],"scalable":[26],"methods":[27,179],"to":[28,64,127,146,180,193,202],"generate":[29],"such":[30,69],"graph":[32,92,184,196],"from":[33,93,143],"these":[34],"alignments.":[35],"Existing":[36],"related":[37],"approaches":[38],"depend":[39],"on":[40,55],"single":[42,132],"reference,":[43],"specific":[45],"ordering":[46],"genomes":[48],"or":[49,239],"de":[51],"Bruijn":[52],"based":[54],"fixed":[57],"k-mer":[58],"length.":[59],"scalable,":[61],"self-contained":[62],"method":[63,191],"build":[65,114,203],"pangenome":[66,77,160,204],"without":[68],"limitations":[70],"would":[71],"be":[72,234],"key":[74],"step":[75],"in":[76,135,169],"construction":[78],"and":[79,98,176,226],"manipulation":[80],"pipelines.":[81],"RESULTS:":[82],"We":[83,102,163,187],"design":[84],"seqwish":[86,212,232],"algorithm,":[87],"which":[88],"builds":[89],"sequences":[97],"between":[100],"them.":[101],"first":[103],"transform":[104],"into":[108,131],"an":[109,165],"implicit":[110],"interval":[111],"tree.":[112],"To":[113],"up":[115],"we":[119,149],"query":[120],"this":[121,156],"tree-based":[122],"representation":[123],"reduce":[128],"transitive":[129],"matches":[130],"segments":[134],"sequence":[137,145],"graph.":[138,162],"By":[139],"recording":[140],"mapping":[142],"input":[144],"output":[147],"can":[150,233],"trace":[151],"original":[153],"paths":[154],"through":[155],"yielding":[158],"present":[164],"implementation":[166],"that":[167,189],"operates":[168],"external":[170],"memory,":[171],"using":[172],"disk-backed":[173],"data":[174],"structures":[175],"lock-free":[177],"parallel":[178],"drive":[181],"core":[183],"induction":[185,197],"step.":[186],"demonstrate":[188],"our":[190],"scales":[192],"very":[194],"large":[195],"problems":[198],"by":[199],"applying":[200],"it":[201],"for":[206],"several":[207],"species.":[208],"AVAILABILITY":[209],"AND":[210],"IMPLEMENTATION:":[211],"is":[213],"published":[214],"as":[215],"free":[216],"software":[217],"under":[218],"MIT":[220],"open":[221],"source":[222],"license.":[223],"Source":[224],"code":[225],"documentation":[227],"available":[229],"at":[230],"https://github.com/ekg/seqwish.":[231],"installed":[235],"via":[236],"Bioconda":[237],"https://bioconda.github.io/recipes/seqwish/README.html":[238],"GNU":[240],"Guix":[241],"https://github.com/ekg/guix-genomics/blob/master/seqwish.scm.":[242]},"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":22},{"year":2023,"cited_by_count":24},{"year":2022,"cited_by_count":4}],"updated_date":"2026-08-10T07:06:39.071514","created_date":"2025-10-10T00:00:00"}
