{"id":"https://openalex.org/W4280583823","doi":"https://doi.org/10.1093/bioinformatics/btac308","title":"ODGI: understanding pangenome graphs","display_name":"ODGI: understanding pangenome graphs","publication_year":2022,"publication_date":"2022-05-10","ids":{"openalex":"https://openalex.org/W4280583823","doi":"https://doi.org/10.1093/bioinformatics/btac308","pmid":"https://pubmed.ncbi.nlm.nih.gov/35552372"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac308","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac308","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/13/3319/44268769/btac308.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/38/13/3319/44268769/btac308.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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 , Milan 20157, Italy"],"raw_orcid":"https://orcid.org/0000-0001-9744-131X","affiliations":[{"raw_affiliation_string":"Genomics Research Centre, Human Technopole , Milan 20157, Italy","institution_ids":["https://openalex.org/I4210115812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040033163","display_name":"Simon Heumos","orcid":"https://orcid.org/0000-0003-3326-817X"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Simon Heumos","raw_affiliation_strings":["Biomedical Data Science, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany","Quantitative Biology Center (QBiC), University of T\u00fcbingen , T\u00fcbingen 72076, Germany"],"raw_orcid":"https://orcid.org/0000-0003-3326-817X","affiliations":[{"raw_affiliation_string":"Biomedical Data Science, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Quantitative Biology Center (QBiC), University of T\u00fcbingen , T\u00fcbingen 72076, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008496386","display_name":"Sven Nahnsen","orcid":"https://orcid.org/0000-0002-4375-0691"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sven Nahnsen","raw_affiliation_strings":["Biomedical Data Science, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany","Quantitative Biology Center (QBiC), University of T\u00fcbingen , T\u00fcbingen 72076, Germany"],"raw_orcid":"https://orcid.org/0000-0002-4375-0691","affiliations":[{"raw_affiliation_string":"Biomedical Data Science, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Quantitative Biology Center (QBiC), University of T\u00fcbingen , T\u00fcbingen 72076, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028085028","display_name":"Pjotr Prins","orcid":"https://orcid.org/0000-0002-8021-9162"},"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":false,"raw_author_name":"Pjotr Prins","raw_affiliation_strings":["Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, USA"],"raw_orcid":null,"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/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"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"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":14.7146,"has_fulltext":true,"cited_by_count":219,"citation_normalized_percentile":{"value":0.9954777,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"38","issue":"13","first_page":"3319","last_page":"3326"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4602000117301941,"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":0.4602000117301941,"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":0.40549999475479126,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.023800000548362732,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42687469720840454}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42687469720840454}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac308","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac308","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/13/3319/44268769/btac308.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:35552372","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35552372","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:9237687","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9237687","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/btac308","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac308","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/13/3319/44268769/btac308.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":[{"display_name":"Partnerships for the goals","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G1147967356","display_name":null,"funder_award_id":"031A533A","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G1159569226","display_name":null,"funder_award_id":"031A534A","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G1254183670","display_name":null,"funder_award_id":"031A538A","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"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/G2082019117","display_name":null,"funder_award_id":"031\u2005A535\u2005A","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G227648021","display_name":null,"funder_award_id":"031 A 534A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2414046978","display_name":null,"funder_award_id":"031A533A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2431772652","display_name":null,"funder_award_id":"031 A538A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2813928278","display_name":null,"funder_award_id":"031\u2005A537B","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G300121295","display_name":null,"funder_award_id":"# 031A537C","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"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/G3603598162","display_name":null,"funder_award_id":"031 A535A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G3681866668","display_name":null,"funder_award_id":"R01 GM123489","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"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/G4848351824","display_name":null,"funder_award_id":"#031A537B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5121333388","display_name":null,"funder_award_id":"031\u2005A532B","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G5139259834","display_name":null,"funder_award_id":"031\u2005A533B","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G5576285491","display_name":null,"funder_award_id":"#031A537C","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G6137013498","display_name":null,"funder_award_id":"2180-390900677","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"},{"id":"https://openalex.org/G8126315642","display_name":null,"funder_award_id":"031A532B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8387372653","display_name":null,"funder_award_id":"031A533B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320323803","display_name":"Bundesministerium f\u00fcr Wirtschaft und Energie","ror":"https://ror.org/02vgg2808"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":"https://ror.org/01vmpm840"},{"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"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4280583823.pdf","grobid_xml":"https://content.openalex.org/works/W4280583823.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1985437611","https://openalex.org/W2066047071","https://openalex.org/W2093610003","https://openalex.org/W2098123284","https://openalex.org/W2102619694","https://openalex.org/W2108234281","https://openalex.org/W2142113273","https://openalex.org/W2153325555","https://openalex.org/W2162923930","https://openalex.org/W2254458779","https://openalex.org/W2255138985","https://openalex.org/W2432815617","https://openalex.org/W2509995029","https://openalex.org/W2547528004","https://openalex.org/W2603734366","https://openalex.org/W2609055977","https://openalex.org/W2797920702","https://openalex.org/W2888300707","https://openalex.org/W2907319204","https://openalex.org/W2940844549","https://openalex.org/W2949102320","https://openalex.org/W2951613337","https://openalex.org/W2952366981","https://openalex.org/W2964697169","https://openalex.org/W2966459122","https://openalex.org/W2966929769","https://openalex.org/W2988098904","https://openalex.org/W3007365321","https://openalex.org/W3012393121","https://openalex.org/W3035986830","https://openalex.org/W3042374389","https://openalex.org/W3042744518","https://openalex.org/W3043054601","https://openalex.org/W3092652421","https://openalex.org/W3100651612","https://openalex.org/W3133795275","https://openalex.org/W3148425969","https://openalex.org/W3165551447","https://openalex.org/W3203118168","https://openalex.org/W4210616455","https://openalex.org/W4220999759","https://openalex.org/W4221127206","https://openalex.org/W4255836900","https://openalex.org/W4281784169","https://openalex.org/W4306809799","https://openalex.org/W4316507600","https://openalex.org/W4379508567"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"MOTIVATION:":[0],"Pangenome":[1],"graphs":[2,41,96,106],"provide":[3],"a":[4,27,78],"complete":[5],"representation":[6,92],"of":[7,11,13,26,36,81,93,100,150],"the":[8,18,22,98,108,164],"mutual":[9],"alignment":[10],"collections":[12],"genomes.":[14],"These":[15],"models":[16],"offer":[17],"opportunity":[19],"to":[20,59,63],"study":[21],"entire":[23],"genomic":[24],"diversity":[25],"population,":[28],"including":[29],"structurally":[30],"complex":[31,118,147],"regions.":[32],"Nevertheless,":[33],"analyzing":[34],"hundreds":[35],"gigabase-scale":[37,151],"genomes":[38],"using":[39],"pangenome":[40,95,152],"is":[42,46,57,158,178],"difficult":[43],"as":[44,139,141,160],"it":[45],"not":[47],"well-supported":[48],"by":[49],"existing":[50],"tools.":[51],"Hence,":[52],"fast":[53,132],"and":[54,87,129,176],"versatile":[55],"software":[56,162],"required":[58],"ask":[60],"advanced":[61],"questions":[62,149],"such":[64],"data":[65,196],"in":[66,97,107],"an":[67,89],"efficient":[68,90],"way.":[69],"RESULTS:":[70],"We":[71],"wrote":[72],"Optimized":[73],"Dynamic":[74],"Genome/Graph":[75],"Implementation":[76],"(ODGI),":[77],"novel":[79],"suite":[80],"tools":[82,115],"that":[83,143],"implements":[84],"scalable":[85],"algorithms":[86],"has":[88],"in-memory":[91],"DNA":[94],"form":[99],"variation":[101],"graphs.":[102,153],"ODGI":[103,113,157,182],"supports":[104],"pre-built":[105],"Graphical":[109],"Fragment":[110],"Assembly":[111],"format.":[112],"includes":[114],"for":[116],"detecting":[117],"regions,":[119],"extracting":[120],"pangenomic":[121,137],"loci,":[122],"removing":[123],"artifacts,":[124],"exploratory":[125],"analysis,":[126],"manipulation,":[127],"validation":[128],"visualization.":[130],"Its":[131],"parallel":[133],"execution":[134],"facilitates":[135],"routine":[136],"tasks,":[138],"well":[140],"pipelines":[142],"can":[144,171,183],"quickly":[145],"answer":[146],"biological":[148],"AVAILABILITY":[154],"AND":[155],"IMPLEMENTATION:":[156],"published":[159],"free":[161],"under":[163],"MIT":[165],"open":[166],"source":[167],"license.":[168],"Source":[169],"code":[170],"be":[172,184],"downloaded":[173],"from":[174],"https://github.com/pangenome/odgi":[175],"documentation":[177],"available":[179,198],"at":[180,199],"https://odgi.readthedocs.io.":[181],"installed":[185],"via":[186],"Bioconda":[187],"https://bioconda.github.io/recipes/odgi/README.html":[188],"or":[189],"GNU":[190],"Guix":[191],"https://github.com/pangenome/odgi/blob/master/guix.scm.":[192],"SUPPLEMENTARY":[193],"INFORMATION:":[194],"Supplementary":[195],"are":[197],"Bioinformatics":[200],"online.":[201]},"counts_by_year":[{"year":2026,"cited_by_count":43},{"year":2025,"cited_by_count":54},{"year":2024,"cited_by_count":77},{"year":2023,"cited_by_count":33},{"year":2022,"cited_by_count":12}],"updated_date":"2026-09-08T07:41:39.490200","created_date":"2025-10-10T00:00:00"}
