{"id":"https://openalex.org/W4283806906","doi":"https://doi.org/10.1093/bioinformatics/btac424","title":"gofasta: command-line utilities for genomic epidemiology research","display_name":"gofasta: command-line utilities for genomic epidemiology research","publication_year":2022,"publication_date":"2022-07-05","ids":{"openalex":"https://openalex.org/W4283806906","doi":"https://doi.org/10.1093/bioinformatics/btac424","pmid":"https://pubmed.ncbi.nlm.nih.gov/35789376"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac424","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac424","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/4033/45300825/btac424.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/38/16/4033/45300825/btac424.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087801737","display_name":"Ben Jackson","orcid":"https://orcid.org/0000-0002-9981-0649"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Ben Jackson","raw_affiliation_strings":["Institute of Ecology and Evolution, University of Edinburgh , Edinburgh EH9 3FL, UK"],"affiliations":[{"raw_affiliation_string":"Institute of Ecology and Evolution, University of Edinburgh , Edinburgh EH9 3FL, UK","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5087801737"],"corresponding_institution_ids":["https://openalex.org/I98677209"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.083,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.8766405,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"38","issue":"16","first_page":"4033","last_page":"4035"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9513000249862671,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9513000249862671,"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/T11243","display_name":"Respiratory viral infections research","score":0.902999997138977,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5641111135482788},{"id":"https://openalex.org/keywords/line","display_name":"Line (geometry)","score":0.49665647745132446},{"id":"https://openalex.org/keywords/epidemiology","display_name":"Epidemiology","score":0.4944419860839844},{"id":"https://openalex.org/keywords/genetic-epidemiology","display_name":"Genetic epidemiology","score":0.4474388360977173},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38497424125671387},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3567744493484497},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26530587673187256},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.20126810669898987},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.07344040274620056},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.06625020503997803}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5641111135482788},{"id":"https://openalex.org/C198352243","wikidata":"https://www.wikidata.org/wiki/Q37105","display_name":"Line (geometry)","level":2,"score":0.49665647745132446},{"id":"https://openalex.org/C107130276","wikidata":"https://www.wikidata.org/wiki/Q133805","display_name":"Epidemiology","level":2,"score":0.4944419860839844},{"id":"https://openalex.org/C177860879","wikidata":"https://www.wikidata.org/wiki/Q5532897","display_name":"Genetic epidemiology","level":3,"score":0.4474388360977173},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38497424125671387},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3567744493484497},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26530587673187256},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.20126810669898987},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.07344040274620056},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.06625020503997803},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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},{"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":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac424","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac424","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/4033/45300825/btac424.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:35789376","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35789376","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:pure.ed.ac.uk:openaire/16bfab8c-cd6c-48bd-b955-4be0062d3cfa","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/16bfab8c-cd6c-48bd-b955-4be0062d3cfa","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Jackson, B & Borgwardt, K (ed.) 2022, 'gofasta : Command-line utilities for genomic epidemiology research', Bioinformatics, vol. 38, no. 16, btac424, pp. 4033-4035. https://doi.org/10.1093/bioinformatics/btac424","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:9364388","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9364388","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/btac424","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac424","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/4033/45300825/btac424.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":[{"id":"https://metadata.un.org/sdg/3","score":0.8100000023841858,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G5984896815","display_name":null,"funder_award_id":"MC_PC_19027","funder_id":"https://openalex.org/F4320319990","funder_display_name":"National Institute for Health and Care Research"}],"funders":[{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4283806906.pdf","grobid_xml":"https://content.openalex.org/works/W4283806906.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W2033339460","https://openalex.org/W2108234281","https://openalex.org/W2144775551","https://openalex.org/W2151409320","https://openalex.org/W2616925143","https://openalex.org/W2765745983","https://openalex.org/W2767318416","https://openalex.org/W2789843538","https://openalex.org/W2950018741","https://openalex.org/W3081341939","https://openalex.org/W3135191472","https://openalex.org/W3180301457","https://openalex.org/W3195311740","https://openalex.org/W3215610096","https://openalex.org/W4312059163","https://openalex.org/W6681367416"],"related_works":["https://openalex.org/W2416509994","https://openalex.org/W1831725511","https://openalex.org/W2398610047","https://openalex.org/W2367858420","https://openalex.org/W2091467237","https://openalex.org/W1479735290","https://openalex.org/W2147480364","https://openalex.org/W2375047670","https://openalex.org/W2136342306","https://openalex.org/W2139623473"],"abstract_inverted_index":{"gofasta":[0],"is":[1],"an":[2],"open-source":[3],"project":[4],"distributed":[5],"under":[6],"the":[7,19,40],"MIT":[8],"license.":[9],"Binaries":[10],"are":[11,37],"available":[12,38],"at":[13],"https://github.com/virus-evolution/gofasta,":[14],"from":[15],"Bioconda,":[16],"and":[17,28],"through":[18],"Go":[20],"programming":[21],"language's":[22],"package":[23],"management":[24],"system.":[25],"Source":[26],"code":[27],"further":[29],"documentation,":[30],"including":[31],"walkthroughs":[32],"for":[33],"common":[34],"use":[35],"cases,":[36],"on":[39],"GitHub":[41],"repository.":[42]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":2}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}