{"id":"https://openalex.org/W3035763183","doi":"https://doi.org/10.1093/bioinformatics/btac176","title":"EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts","display_name":"EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts","publication_year":2022,"publication_date":"2022-03-24","ids":{"openalex":"https://openalex.org/W3035763183","doi":"https://doi.org/10.1093/bioinformatics/btac176","mag":"3035763183","pmid":"https://pubmed.ncbi.nlm.nih.gov/35561186"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac176","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac176","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2700/43705090/btac176.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2700/43705090/btac176.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073354692","display_name":"Chien\u2010Chi Lo","orcid":"https://orcid.org/0000-0003-3470-1078"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chien-Chi Lo","raw_affiliation_strings":["Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"],"raw_orcid":"https://orcid.org/0000-0003-3470-1078","affiliations":[{"raw_affiliation_string":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087166268","display_name":"Migun Shakya","orcid":"https://orcid.org/0000-0003-3876-691X"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Migun Shakya","raw_affiliation_strings":["Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"],"raw_orcid":"https://orcid.org/0000-0003-3876-691X","affiliations":[{"raw_affiliation_string":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023084976","display_name":"Ryan Connor","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Connor","raw_affiliation_strings":["National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health , Bethesda, MD 20894, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health , Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059872543","display_name":"Karen W. Davenport","orcid":"https://orcid.org/0000-0002-2740-1344"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karen Davenport","raw_affiliation_strings":["Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022176874","display_name":"Mark Flynn","orcid":"https://orcid.org/0000-0002-6162-9510"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Flynn","raw_affiliation_strings":["Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061894573","display_name":"Ad\u00e1n Myers y Guti\u00e9rrez","orcid":"https://orcid.org/0000-0002-3457-1632"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ad\u00e1n Myers y Guti\u00e9rrez","raw_affiliation_strings":["Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"],"raw_orcid":"https://orcid.org/0000-0002-3457-1632","affiliations":[{"raw_affiliation_string":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043402436","display_name":"Bin Hu","orcid":"https://orcid.org/0000-0002-0278-8466"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bin Hu","raw_affiliation_strings":["Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"],"raw_orcid":"https://orcid.org/0000-0002-0278-8466","affiliations":[{"raw_affiliation_string":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020658723","display_name":"Po\u2010E Li","orcid":"https://orcid.org/0000-0003-4290-1993"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Po-E Li","raw_affiliation_strings":["Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004400351","display_name":"Elais Player Jackson","orcid":null},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elais Player Jackson","raw_affiliation_strings":["Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101608392","display_name":"Yan Xu","orcid":"https://orcid.org/0009-0005-8274-8681"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yan Xu","raw_affiliation_strings":["Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006014190","display_name":"Patrick Chain","orcid":"https://orcid.org/0000-0003-3949-3634"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Patrick S G Chain","raw_affiliation_strings":["Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006014190","https://openalex.org/A5073354692"],"corresponding_institution_ids":["https://openalex.org/I1343871089"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.9587,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.86618361,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"10","first_page":"2700","last_page":"2704"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7843999862670898,"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":0.7843999862670898,"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/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.12080000340938568,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.012299999594688416,"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/workflow","display_name":"Workflow","score":0.7152218222618103},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5531248450279236},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4943113327026367},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4924381673336029},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.46284765005111694},{"id":"https://openalex.org/keywords/minion","display_name":"Minion","score":0.4593390226364136},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4415067434310913},{"id":"https://openalex.org/keywords/genbank","display_name":"GenBank","score":0.41486459970474243},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3474307060241699},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32036080956459045},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31380489468574524},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.28760427236557007},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26145708560943604},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.22882899641990662}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7152218222618103},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5531248450279236},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4943113327026367},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4924381673336029},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.46284765005111694},{"id":"https://openalex.org/C2779927696","wikidata":"https://www.wikidata.org/wiki/Q6865654","display_name":"Minion","level":5,"score":0.4593390226364136},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4415067434310913},{"id":"https://openalex.org/C79029880","wikidata":"https://www.wikidata.org/wiki/Q901755","display_name":"GenBank","level":3,"score":0.41486459970474243},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3474307060241699},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32036080956459045},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31380489468574524},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.28760427236557007},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26145708560943604},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.22882899641990662},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"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":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","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":"D058873","descriptor_name":"Pandemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/btac176","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac176","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2700/43705090/btac176.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35561186","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35561186","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:osti.gov:1861895","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1861895","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:1868101","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1868101","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:2470536","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2470536","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:2477218","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2477218","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9113274","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9113274","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac176","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac176","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2700/43705090/btac176.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6600000262260437,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1736759198","display_name":null,"funder_award_id":"20200732ER","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G3434090788","display_name":null,"funder_award_id":"KP160101","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G367708065","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5235667075","display_name":null,"funder_award_id":"CB10152","funder_id":"https://openalex.org/F4320332186","funder_display_name":"Defense Threat Reduction Agency"},{"id":"https://openalex.org/G742420055","display_name":null,"funder_award_id":"4000150817","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7759721646","display_name":null,"funder_award_id":"MCB180107","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G783087351","display_name":null,"funder_award_id":"CB10623","funder_id":"https://openalex.org/F4320332186","funder_display_name":"Defense Threat Reduction Agency"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332186","display_name":"Defense Threat Reduction Agency","ror":"https://ror.org/04tz64554"},{"id":"https://openalex.org/F4320337547","display_name":"Laboratory Directed Research and Development","ror":"https://ror.org/01e41cf67"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3035763183.pdf","grobid_xml":"https://content.openalex.org/works/W3035763183.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2079958213","https://openalex.org/W2336957559","https://openalex.org/W2558135510","https://openalex.org/W2605343262","https://openalex.org/W2789843538","https://openalex.org/W2883511460","https://openalex.org/W2951149781","https://openalex.org/W3160568774","https://openalex.org/W3180301457","https://openalex.org/W3204754419","https://openalex.org/W4255659575"],"related_works":["https://openalex.org/W4247233796","https://openalex.org/W2948357900","https://openalex.org/W4404395053","https://openalex.org/W2774863662","https://openalex.org/W2124499964","https://openalex.org/W2749851556","https://openalex.org/W2765793069","https://openalex.org/W2887783619","https://openalex.org/W1920720327","https://openalex.org/W2515795842"],"abstract_inverted_index":{"SUMMARY:":[0],"Genomics":[1],"has":[2],"become":[3],"an":[4,112],"essential":[5],"technology":[6],"for":[7,19,40,49,73],"surveilling":[8],"emerging":[9],"infectious":[10],"disease":[11],"outbreaks.":[12],"A":[13,44],"range":[14],"of":[15,97,163],"technologies":[16,209],"and":[17,23,34,76,86,126,131,140,146,159,165,172,202,213,219],"strategies":[18],"pathogen":[20],"genome":[21,42,54,124],"enrichment":[22],"sequencing":[24,99],"are":[25,225],"being":[26],"used":[27],"by":[28],"laboratories":[29],"worldwide,":[30],"together":[31],"with":[32,102,177,205],"different":[33],"sometimes":[35],"ad":[36],"hoc,":[37],"analytical":[38,47],"procedures":[39],"generating":[41],"sequences.":[43],"fully":[45],"integrated":[46,87],"process":[48],"raw":[50,148],"sequence":[51,139],"to":[52,57,67,92,135,143],"consensus":[53,127,138],"determination,":[55],"suited":[56],"outbreaks":[58],"such":[59],"as":[60],"the":[61,104,133,137,161,180],"ongoing":[62],"COVID-19":[63,181],"pandemic,":[64],"is":[65],"critical":[66],"provide":[68,93],"a":[69,83,198],"solid":[70],"genomic":[71],"basis":[72],"epidemiological":[74],"analyses":[75,186],"well-informed":[77],"decision":[78],"making.":[79],"We":[80,151],"have":[81],"developed":[82],"web-based":[84,114],"platform":[85],"bioinformatic":[88],"workflows":[89,190],"that":[90,188],"help":[91],"consistent":[94],"high-quality":[95,192],"analysis":[96,167],"SARS-CoV-2":[98,122,193],"data":[100,119,149,158,224],"generated":[101],"either":[103],"Illumina":[105,206],"or":[106],"Oxford":[107],"Nanopore":[108],"Technologies":[109],"(ONT).":[110],"Using":[111],"intuitive":[113],"interface,":[115],"this":[116],"workflow":[117,153,211],"automates":[118],"quality":[120],"control,":[121],"reference-based":[123],"variant":[125,164],"calling,":[128],"lineage":[129,166],"determination":[130],"provides":[132],"ability":[134],"submit":[136],"necessary":[141],"metadata":[142],"GenBank,":[144],"GISAID":[145],"INSDC":[147],"repositories.":[150],"tested":[152],"usability":[154],"using":[155,168],"real":[156],"world":[157],"validated":[160],"accuracy":[162],"several":[169],"test":[170],"datasets,":[171],"further":[173],"performed":[174],"detailed":[175],"comparisons":[176],"results":[178],"from":[179],"Galaxy":[182],"Project":[183],"workflow.":[184],"Our":[185],"indicate":[187],"EC-19":[189],"generate":[191],"genomes.":[194],"Finally,":[195],"we":[196],"share":[197],"perspective":[199],"on":[200,210],"patterns":[201],"impact":[203],"observed":[204],"versus":[207],"ONT":[208],"congruence":[212],"differences.":[214],"AVAILABILITY":[215],"AND":[216],"IMPLEMENTATION:":[217],"https://edge-covid19.edgebioinformatics.org,":[218],"https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2.":[220],"SUPPLEMENTARY":[221],"INFORMATION:":[222],"Supplementary":[223],"available":[226],"at":[227],"Bioinformatics":[228],"online.":[229]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2020-06-19T00:00:00"}
