{"id":"https://openalex.org/W4311663808","doi":"https://doi.org/10.1093/bioinformatics/btac808","title":"YaHS: yet another Hi-C scaffolding tool","display_name":"YaHS: yet another Hi-C scaffolding tool","publication_year":2022,"publication_date":"2022-12-16","ids":{"openalex":"https://openalex.org/W4311663808","doi":"https://doi.org/10.1093/bioinformatics/btac808","pmid":"https://pubmed.ncbi.nlm.nih.gov/36525368"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac808","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac808","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac808/48763581/btac808.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/btac808/48763581/btac808.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022826861","display_name":"Chenxi Zhou","orcid":"https://orcid.org/0000-0002-1735-2630"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Chenxi Zhou","raw_affiliation_strings":["Department of Genetics, University of Cambridge , Cambridge CB2 3EH, UK","Wellcome Sanger Institute, Wellcome Genome Campus , Cambridge CB10 1SA, UK"],"raw_orcid":"https://orcid.org/0000-0002-1735-2630","affiliations":[{"raw_affiliation_string":"Department of Genetics, University of Cambridge , Cambridge CB2 3EH, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus , Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030669774","display_name":"Shane McCarthy","orcid":"https://orcid.org/0000-0002-2715-4187"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shane A McCarthy","raw_affiliation_strings":["Department of Genetics, University of Cambridge , Cambridge CB2 3EH, UK","Wellcome Sanger Institute, Wellcome Genome Campus , Cambridge CB10 1SA, UK"],"raw_orcid":"https://orcid.org/0000-0002-2715-4187","affiliations":[{"raw_affiliation_string":"Department of Genetics, University of Cambridge , Cambridge CB2 3EH, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus , Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082040351","display_name":"Richard Durbin","orcid":"https://orcid.org/0000-0002-9130-1006"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Richard Durbin","raw_affiliation_strings":["Department of Genetics, University of Cambridge , Cambridge CB2 3EH, UK","Wellcome Sanger Institute, Wellcome Genome Campus , Cambridge CB10 1SA, UK"],"raw_orcid":"https://orcid.org/0000-0002-9130-1006","affiliations":[{"raw_affiliation_string":"Department of Genetics, University of Cambridge , Cambridge CB2 3EH, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus , Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5082040351"],"corresponding_institution_ids":["https://openalex.org/I241749","https://openalex.org/I2802476451"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":147.0096,"has_fulltext":true,"cited_by_count":2426,"citation_normalized_percentile":{"value":0.99993418,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"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":0.79830002784729,"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":0.79830002784729,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.026100000366568565,"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/T10604","display_name":"RNA Research and Splicing","score":0.01899999938905239,"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":0.8192871809005737},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.7393555641174316},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6625899076461792},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6105412244796753},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5804920792579651},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5307599902153015},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.451985239982605},{"id":"https://openalex.org/keywords/codebase","display_name":"Codebase","score":0.43562647700309753},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.37836509943008423},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3751427233219147},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.33924806118011475},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.15523424744606018}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8192871809005737},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.7393555641174316},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6625899076461792},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6105412244796753},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5804920792579651},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5307599902153015},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.451985239982605},{"id":"https://openalex.org/C51929080","wikidata":"https://www.wikidata.org/wiki/Q2425187","display_name":"Codebase","level":3,"score":0.43562647700309753},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.37836509943008423},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3751427233219147},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.33924806118011475},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.15523424744606018}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac808","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac808","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac808/48763581/btac808.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:36525368","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36525368","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:9848053","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9848053","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/btac808","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac808","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac808/48763581/btac808.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/G1101290722","display_name":"Whole genome sequence based analysis of genetic variation and genome evolution","funder_award_id":"207492","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G313278666","display_name":"Darwin Tree of Life","funder_award_id":"218328","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G4097197391","display_name":"Whole genome sequence based analysis of genetic variation and genome evolution","funder_award_id":"207492/Z/17/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G5218641380","display_name":"Wellcome Sanger Institute Quinquennial Review 2021-2026","funder_award_id":"220540","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4311663808.pdf","grobid_xml":"https://content.openalex.org/works/W4311663808.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1489349053","https://openalex.org/W2090037139","https://openalex.org/W2118970626","https://openalex.org/W2396077153","https://openalex.org/W2493763501","https://openalex.org/W2802282671","https://openalex.org/W2808352813","https://openalex.org/W2948330847","https://openalex.org/W2965879979","https://openalex.org/W2969330652","https://openalex.org/W2999262337","https://openalex.org/W3007172120","https://openalex.org/W3159728495","https://openalex.org/W3216110456","https://openalex.org/W4205493727","https://openalex.org/W4220999759","https://openalex.org/W6763263287","https://openalex.org/W6804054412","https://openalex.org/W6805839138"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2546377002","https://openalex.org/W4285209474","https://openalex.org/W2344367508","https://openalex.org/W22571951","https://openalex.org/W2046541848","https://openalex.org/W2571988079","https://openalex.org/W2791776396","https://openalex.org/W2117798581","https://openalex.org/W4384009753"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"present":[2],"YaHS,":[3],"a":[4,22],"user-friendly":[5],"command-line":[6],"tool":[7],"for":[8],"the":[9,77],"construction":[10,56],"of":[11,57],"chromosome-scale":[12],"scaffolds":[13],"from":[14,28],"Hi-C":[15],"data.":[16],"It":[17],"can":[18],"be":[19],"run":[20],"with":[21,40,61],"single-line":[23],"command,":[24],"requires":[25],"minimal":[26],"input":[27],"users":[29],"(an":[30],"assembly":[31,45],"file":[32],"and":[33,43,54,64,74,84],"an":[34],"alignment":[35],"file)":[36],"which":[37],"is":[38,70],"compatible":[39],"similar":[41],"tools":[42],"provides":[44],"results":[46],"in":[47,72],"multiple":[48],"formats,":[49],"thereby":[50],"enabling":[51],"rapid,":[52],"robust":[53],"scalable":[55],"high-quality":[58],"genome":[59],"assemblies":[60],"high":[62],"accuracy":[63],"contiguity.":[65],"AVAILABILITY":[66],"AND":[67],"IMPLEMENTATION:":[68],"YaHS":[69],"implemented":[71],"C":[73],"licensed":[75],"under":[76],"MIT":[78],"License.":[79],"The":[80],"source":[81],"code,":[82],"documentation":[83],"tutorial":[85],"are":[86,94],"available":[87,95],"at":[88,96],"https://github.com/sanger-tol/yahs.":[89],"SUPPLEMENTARY":[90],"INFORMATION:":[91],"Supplementary":[92],"data":[93],"Bioinformatics":[97],"online.":[98]},"counts_by_year":[{"year":2026,"cited_by_count":550},{"year":2025,"cited_by_count":828},{"year":2024,"cited_by_count":707},{"year":2023,"cited_by_count":323},{"year":2022,"cited_by_count":18}],"updated_date":"2026-08-14T07:06:38.338062","created_date":"2025-10-10T00:00:00"}
