{"id":"https://openalex.org/W4408212705","doi":"https://doi.org/10.1093/bioinformatics/btaf102","title":"PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance","display_name":"PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance","publication_year":2025,"publication_date":"2025-03-07","ids":{"openalex":"https://openalex.org/W4408212705","doi":"https://doi.org/10.1093/bioinformatics/btaf102","pmid":"https://pubmed.ncbi.nlm.nih.gov/40053686"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf102","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf102","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf102/62340404/btaf102.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf102/62340404/btaf102.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018899263","display_name":"Gabriele Leoni","orcid":"https://orcid.org/0000-0001-8269-3127"},"institutions":[{"id":"https://openalex.org/I2800387288","display_name":"European Commission","ror":"https://ror.org/00k4n6c32","country_code":"BE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288"]},{"id":"https://openalex.org/I4210118689","display_name":"Joint Research Centre","ror":"https://ror.org/02qezmz13","country_code":"IT","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210118689","https://openalex.org/I4210161702"]},{"id":"https://openalex.org/I4210133948","display_name":"Joint Research Centre","ror":"https://ror.org/02ptz5951","country_code":"DE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210133948","https://openalex.org/I4210161702"]}],"countries":["BE","DE","IT"],"is_corresponding":true,"raw_author_name":"Gabriele Leoni","raw_affiliation_strings":["European Commission, Joint Research Centre (JRC) , Ispra, 21027,","European Commission, Joint Research Centre (JRC), Ispra, Italy"],"affiliations":[{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC) , Ispra, 21027,","institution_ids":["https://openalex.org/I2800387288","https://openalex.org/I4210133948"]},{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC), Ispra, Italy","institution_ids":["https://openalex.org/I4210118689"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015889163","display_name":"Mauro Petrillo","orcid":"https://orcid.org/0000-0002-6782-4704"},"institutions":[{"id":"https://openalex.org/I4210087530","display_name":"Eidos (Italy)","ror":"https://ror.org/0033e0z76","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210087530"]},{"id":"https://openalex.org/I4210166283","display_name":"Eidon (Italy)","ror":"https://ror.org/023dbr455","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210166283"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mauro Petrillo","raw_affiliation_strings":["Seidor Italy S.r.l. , Milan, 20122,","Seidor Italy S.r.l, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Seidor Italy S.r.l. , Milan, 20122,","institution_ids":["https://openalex.org/I4210166283"]},{"raw_affiliation_string":"Seidor Italy S.r.l, Milan, Italy","institution_ids":["https://openalex.org/I4210087530"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073423716","display_name":"Violeta Serra","orcid":"https://orcid.org/0000-0001-6620-1065"},"institutions":[{"id":"https://openalex.org/I2800387288","display_name":"European Commission","ror":"https://ror.org/00k4n6c32","country_code":"BE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288"]},{"id":"https://openalex.org/I4210133948","display_name":"Joint Research Centre","ror":"https://ror.org/02ptz5951","country_code":"DE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210133948","https://openalex.org/I4210161702"]},{"id":"https://openalex.org/I4210162697","display_name":"Joint Research Centre","ror":"https://ror.org/05wzskb47","country_code":"NL","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210161702","https://openalex.org/I4210162697"]}],"countries":["BE","DE","NL"],"is_corresponding":false,"raw_author_name":"Victoria Ruiz-Serra","raw_affiliation_strings":["European Commission, Joint Research Centre (JRC) , Geel, 2440,","European Commission, Joint Research Centre (JRC), Geel, Belgium"],"affiliations":[{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC) , Geel, 2440,","institution_ids":["https://openalex.org/I2800387288","https://openalex.org/I4210133948","https://openalex.org/I4210162697"]},{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC), Geel, Belgium","institution_ids":["https://openalex.org/I2800387288"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021621479","display_name":"Maddalena Querci","orcid":"https://orcid.org/0000-0002-0788-1627"},"institutions":[{"id":"https://openalex.org/I2800387288","display_name":"European Commission","ror":"https://ror.org/00k4n6c32","country_code":"BE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288"]},{"id":"https://openalex.org/I4210118689","display_name":"Joint Research Centre","ror":"https://ror.org/02qezmz13","country_code":"IT","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210118689","https://openalex.org/I4210161702"]},{"id":"https://openalex.org/I4210133948","display_name":"Joint Research Centre","ror":"https://ror.org/02ptz5951","country_code":"DE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210133948","https://openalex.org/I4210161702"]}],"countries":["BE","DE","IT"],"is_corresponding":false,"raw_author_name":"Maddalena Querci","raw_affiliation_strings":["European Commission, Joint Research Centre (JRC) , Ispra, 21027,","European Commission, Joint Research Centre (JRC), Ispra, Italy"],"affiliations":[{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC) , Ispra, 21027,","institution_ids":["https://openalex.org/I2800387288","https://openalex.org/I4210133948"]},{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC), Ispra, Italy","institution_ids":["https://openalex.org/I4210118689"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021936550","display_name":"Sandra Coecke","orcid":"https://orcid.org/0000-0003-2773-6408"},"institutions":[{"id":"https://openalex.org/I2800387288","display_name":"European Commission","ror":"https://ror.org/00k4n6c32","country_code":"BE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288"]},{"id":"https://openalex.org/I4210118689","display_name":"Joint Research Centre","ror":"https://ror.org/02qezmz13","country_code":"IT","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210118689","https://openalex.org/I4210161702"]},{"id":"https://openalex.org/I4210133948","display_name":"Joint Research Centre","ror":"https://ror.org/02ptz5951","country_code":"DE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210133948","https://openalex.org/I4210161702"]}],"countries":["BE","DE","IT"],"is_corresponding":false,"raw_author_name":"Sandra Coecke","raw_affiliation_strings":["European Commission, Joint Research Centre (JRC) , Ispra, 21027,","European Commission, Joint Research Centre (JRC), Ispra, Italy"],"affiliations":[{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC) , Ispra, 21027,","institution_ids":["https://openalex.org/I2800387288","https://openalex.org/I4210133948"]},{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC), Ispra, Italy","institution_ids":["https://openalex.org/I4210118689"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073593736","display_name":"Tobias Wiesenthal","orcid":null},"institutions":[{"id":"https://openalex.org/I2800387288","display_name":"European Commission","ror":"https://ror.org/00k4n6c32","country_code":"BE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288"]},{"id":"https://openalex.org/I4210133948","display_name":"Joint Research Centre","ror":"https://ror.org/02ptz5951","country_code":"DE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210133948","https://openalex.org/I4210161702"]},{"id":"https://openalex.org/I4210162697","display_name":"Joint Research Centre","ror":"https://ror.org/05wzskb47","country_code":"NL","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210161702","https://openalex.org/I4210162697"]}],"countries":["BE","DE","NL"],"is_corresponding":false,"raw_author_name":"Tobias Wiesenthal","raw_affiliation_strings":["European Commission, Joint Research Centre (JRC) , Geel, 2440,","European Commission, Joint Research Centre (JRC), Geel, Belgium"],"affiliations":[{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC) , Geel, 2440,","institution_ids":["https://openalex.org/I2800387288","https://openalex.org/I4210133948","https://openalex.org/I4210162697"]},{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC), Geel, Belgium","institution_ids":["https://openalex.org/I2800387288"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5018899263"],"corresponding_institution_ids":["https://openalex.org/I2800387288","https://openalex.org/I4210118689","https://openalex.org/I4210133948"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.5591,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.80756179,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"41","issue":"4","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":0.998199999332428,"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":0.998199999332428,"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/T11688","display_name":"Microbial infections and disease research","score":0.9908999800682068,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.986299991607666,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.804051399230957},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6718161106109619},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.5395383834838867},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.535297691822052},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5264352560043335},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.46806231141090393},{"id":"https://openalex.org/keywords/data-quality","display_name":"Data quality","score":0.42945486307144165},{"id":"https://openalex.org/keywords/pace","display_name":"Pace","score":0.42647111415863037},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3714701235294342},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.23317748308181763},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2195434868335724},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1396726667881012},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09729349613189697}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.804051399230957},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6718161106109619},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.5395383834838867},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.535297691822052},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5264352560043335},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.46806231141090393},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.42945486307144165},{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.42647111415863037},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3714701235294342},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.23317748308181763},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2195434868335724},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1396726667881012},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09729349613189697},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"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":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"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":"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":true},{"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":true},{"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":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf102","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf102","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf102/62340404/btaf102.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:40053686","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40053686","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:europepmc.org:10774794","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11961196","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf102","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf102","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf102/62340404/btaf102.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408212705.pdf"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1964807436","https://openalex.org/W2168133698","https://openalex.org/W2895413049","https://openalex.org/W2951912016","https://openalex.org/W2952946229","https://openalex.org/W2969876541","https://openalex.org/W3003217347","https://openalex.org/W3004280078","https://openalex.org/W3047632937","https://openalex.org/W3131055609","https://openalex.org/W3136850423","https://openalex.org/W3158324281","https://openalex.org/W3164567672","https://openalex.org/W3180301457","https://openalex.org/W3186583873","https://openalex.org/W4200137031","https://openalex.org/W4210285301","https://openalex.org/W4221076849","https://openalex.org/W4223916144","https://openalex.org/W4229082025","https://openalex.org/W4283799942","https://openalex.org/W4284696817","https://openalex.org/W4294578363","https://openalex.org/W4317241210","https://openalex.org/W4362609000","https://openalex.org/W4379185238","https://openalex.org/W4385486940","https://openalex.org/W4386618952","https://openalex.org/W4392646825","https://openalex.org/W4402990601","https://openalex.org/W6806254383","https://openalex.org/W6850086644"],"related_works":["https://openalex.org/W2386723501","https://openalex.org/W2387879414","https://openalex.org/W2390304029","https://openalex.org/W2341492732","https://openalex.org/W2354923724","https://openalex.org/W3187193180","https://openalex.org/W2146830340","https://openalex.org/W2377101853","https://openalex.org/W3033117735","https://openalex.org/W2746208547"],"abstract_inverted_index":{"PathoSeq-QC":[0],"is":[1,12],"a":[2],"command-line":[3],"tool":[4],"written":[5],"in":[6],"Python":[7],"and":[8],"R.":[9],"The":[10],"code":[11],"available":[13],"at":[14],"https://code.europa.eu/dighealth/pathoseq-qc.":[15]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-06T07:47:59.780226","created_date":"2025-10-10T00:00:00"}
