{"id":"https://openalex.org/W4404442821","doi":"https://doi.org/10.1093/bib/bbae597","title":"MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data","display_name":"MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4404442821","doi":"https://doi.org/10.1093/bib/bbae597","pmid":"https://pubmed.ncbi.nlm.nih.gov/39550223"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae597","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae597","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbae597","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049999884","display_name":"Martin Bosilj","orcid":"https://orcid.org/0000-0002-4663-9622"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]},{"id":"https://openalex.org/I4210122847","display_name":"Czech Academy of Sciences, Institute of Microbiology","ror":"https://ror.org/02p1jz666","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}],"countries":["CZ","SI"],"is_corresponding":false,"raw_author_name":"Martin Bosilj","raw_affiliation_strings":["Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,"],"raw_orcid":"https://orcid.org/0000-0002-4663-9622","affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I4210122847"]},{"raw_affiliation_string":"University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058895573","display_name":"Alen Sulji\u010d","orcid":"https://orcid.org/0000-0002-4596-7931"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]},{"id":"https://openalex.org/I4210122847","display_name":"Czech Academy of Sciences, Institute of Microbiology","ror":"https://ror.org/02p1jz666","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}],"countries":["CZ","SI"],"is_corresponding":false,"raw_author_name":"Alen Sulji\u010d","raw_affiliation_strings":["Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,"],"raw_orcid":"https://orcid.org/0000-0002-4596-7931","affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I4210122847"]},{"raw_affiliation_string":"University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074916584","display_name":"Samo Zakotnik","orcid":"https://orcid.org/0000-0002-0478-2009"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]},{"id":"https://openalex.org/I4210122847","display_name":"Czech Academy of Sciences, Institute of Microbiology","ror":"https://ror.org/02p1jz666","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}],"countries":["CZ","SI"],"is_corresponding":false,"raw_author_name":"Samo Zakotnik","raw_affiliation_strings":["Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I4210122847"]},{"raw_affiliation_string":"University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038052863","display_name":"Jan Slune\u010dko","orcid":null},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]},{"id":"https://openalex.org/I4210122847","display_name":"Czech Academy of Sciences, Institute of Microbiology","ror":"https://ror.org/02p1jz666","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}],"countries":["CZ","SI"],"is_corresponding":false,"raw_author_name":"Jan Slune\u010dko","raw_affiliation_strings":["Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I4210122847"]},{"raw_affiliation_string":"University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056379783","display_name":"Rok Kogoj","orcid":"https://orcid.org/0000-0002-8999-4923"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]},{"id":"https://openalex.org/I4210122847","display_name":"Czech Academy of Sciences, Institute of Microbiology","ror":"https://ror.org/02p1jz666","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}],"countries":["CZ","SI"],"is_corresponding":false,"raw_author_name":"Rok Kogoj","raw_affiliation_strings":["Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I4210122847"]},{"raw_affiliation_string":"University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053527974","display_name":"Mi\u0161a Korva","orcid":"https://orcid.org/0000-0003-1501-1004"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]},{"id":"https://openalex.org/I4210122847","display_name":"Czech Academy of Sciences, Institute of Microbiology","ror":"https://ror.org/02p1jz666","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}],"countries":["CZ","SI"],"is_corresponding":false,"raw_author_name":"Misa Korva","raw_affiliation_strings":["Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,"],"raw_orcid":"https://orcid.org/0000-0003-1501-1004","affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Immunology , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I4210122847"]},{"raw_affiliation_string":"University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka cesta 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I153976015"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.9502,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.75033635,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"25","issue":"6","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":0.9991000294685364,"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":0.9991000294685364,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9945999979972839,"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"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9930999875068665,"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/metagenomics","display_name":"Metagenomics","score":0.918036699295044},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8255618810653687},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5798628330230713},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.4613177478313446},{"id":"https://openalex.org/keywords/clinical-microbiology","display_name":"Clinical microbiology","score":0.42937445640563965},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4280935525894165},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39345604181289673},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3693721890449524},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2423558533191681},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15848860144615173},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.15066209435462952},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11529147624969482},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.08671325445175171}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.918036699295044},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8255618810653687},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5798628330230713},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.4613177478313446},{"id":"https://openalex.org/C2992965680","wikidata":"https://www.wikidata.org/wiki/Q598976","display_name":"Clinical microbiology","level":2,"score":0.42937445640563965},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4280935525894165},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39345604181289673},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3693721890449524},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2423558533191681},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15848860144615173},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.15066209435462952},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11529147624969482},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.08671325445175171}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"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":false},{"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":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","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":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbae597","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae597","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39550223","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39550223","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11568877","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11568877","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11568877/pdf/bbae597.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:d.cobiss.net/repository/si:217049091","is_oa":true,"landing_page_url":"https://academic.oup.com/bib/article/25/6/bbae597/7901732?login=false","pdf_url":null,"source":{"id":"https://openalex.org/S7407055177","display_name":"dCOBISS.SI Digital Repository","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"COBISS-ID: 3210260","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae597","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae597","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.44999998807907104}],"awards":[],"funders":[{"id":"https://openalex.org/F4320324592","display_name":"Univerza v Ljubljani","ror":"https://ror.org/05njb9z20"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":85,"referenced_works":["https://openalex.org/W1886475448","https://openalex.org/W1974764034","https://openalex.org/W1994910068","https://openalex.org/W1995478592","https://openalex.org/W2029343630","https://openalex.org/W2050820276","https://openalex.org/W2075126870","https://openalex.org/W2085926377","https://openalex.org/W2103441770","https://openalex.org/W2128964206","https://openalex.org/W2137662380","https://openalex.org/W2140466960","https://openalex.org/W2166395958","https://openalex.org/W2170551349","https://openalex.org/W2175526948","https://openalex.org/W2326713239","https://openalex.org/W2432815617","https://openalex.org/W2599417231","https://openalex.org/W2613409207","https://openalex.org/W2644577350","https://openalex.org/W2730233141","https://openalex.org/W2736894590","https://openalex.org/W2742837602","https://openalex.org/W2750586496","https://openalex.org/W2795291274","https://openalex.org/W2890665816","https://openalex.org/W2899761875","https://openalex.org/W2903912375","https://openalex.org/W2917706989","https://openalex.org/W2950964375","https://openalex.org/W2951160681","https://openalex.org/W2951278111","https://openalex.org/W2952402079","https://openalex.org/W2968450569","https://openalex.org/W2969316324","https://openalex.org/W2970997288","https://openalex.org/W2977180444","https://openalex.org/W2983165568","https://openalex.org/W2985444402","https://openalex.org/W2990618091","https://openalex.org/W2996645820","https://openalex.org/W3000477794","https://openalex.org/W3004280078","https://openalex.org/W3005510968","https://openalex.org/W3027089056","https://openalex.org/W3049091217","https://openalex.org/W3075003134","https://openalex.org/W3091506611","https://openalex.org/W3092684668","https://openalex.org/W3099584446","https://openalex.org/W3105281758","https://openalex.org/W3122109253","https://openalex.org/W3131055609","https://openalex.org/W3135354469","https://openalex.org/W3144346147","https://openalex.org/W3153029086","https://openalex.org/W3162965417","https://openalex.org/W3174210264","https://openalex.org/W3188360386","https://openalex.org/W3202634790","https://openalex.org/W3202712630","https://openalex.org/W3212458738","https://openalex.org/W4211164325","https://openalex.org/W4225258284","https://openalex.org/W4282932758","https://openalex.org/W4283018586","https://openalex.org/W4284881286","https://openalex.org/W4285592078","https://openalex.org/W4289274885","https://openalex.org/W4294916321","https://openalex.org/W4297425340","https://openalex.org/W4297498241","https://openalex.org/W4297723515","https://openalex.org/W4297969096","https://openalex.org/W4308195917","https://openalex.org/W4308786520","https://openalex.org/W4309506895","https://openalex.org/W4311305969","https://openalex.org/W4313824304","https://openalex.org/W4367668614","https://openalex.org/W4386372879","https://openalex.org/W4386377254","https://openalex.org/W4387895255","https://openalex.org/W4390747654","https://openalex.org/W4391986707"],"related_works":["https://openalex.org/W1994449010","https://openalex.org/W2330186985","https://openalex.org/W2950447380","https://openalex.org/W2055448750","https://openalex.org/W2345730070","https://openalex.org/W2107854630","https://openalex.org/W4319294554","https://openalex.org/W3134563641","https://openalex.org/W1986608492","https://openalex.org/W4394186879"],"abstract_inverted_index":{"Over":[0],"the":[1,10,21,43,47,59,93,96,118,198,205],"past":[2],"decade,":[3],"there":[4],"have":[5],"been":[6],"many":[7],"improvements":[8],"in":[9,18,134,161,177,183,224],"field":[11],"of":[12,23,46,63,95,207,221],"metagenomics,":[13],"including":[14],"sequencing":[15,29],"technologies,":[16],"advances":[17],"bioinformatics":[19,31,44],"and":[20,30,61,66,85,107,155,164,168,213],"development":[22],"reference":[24,215],"databases,":[25],"but":[26,136],"a":[27,54,76,190],"one-size-fits-all":[28],"pipeline":[32],"does":[33],"not":[34,188],"yet":[35],"seem":[36],"achievable.":[37],"In":[38,139,149,180],"this":[39,140,202],"study,":[40],"we":[41],"address":[42],"part":[45],"analysis":[48],"by":[49],"combining":[50,208],"three":[51],"methods":[52],"into":[53,75],"three-step":[55],"workflow":[56,78],"that":[57],"increases":[58],"sensitivity":[60],"specificity":[62],"clinical":[64,101,225],"metagenomics":[65,89],"improves":[67],"pathogen":[68,121],"detection.":[69],"The":[70],"individual":[71],"tools":[72],"are":[73],"combined":[74],"user-friendly":[77],"suitable":[79],"for":[80,217],"analysing":[81],"short":[82],"paired-end":[83],"(PE)":[84],"long":[86],"reads":[87],"from":[88,111],"datasets-MetaAll.":[90],"To":[91],"demonstrate":[92],"applicability":[94],"developed":[97],"workflow,":[98],"four":[99],"complicated":[100],"cases":[102],"with":[103,152,166],"different":[104,112],"disease":[105],"presentations":[106],"multiple":[108],"samples":[109],"collected":[110],"biological":[113],"sites":[114],"as":[115,117,197],"well":[116],"CAMI":[119],"Clinical":[120],"detection":[122,220],"challenge":[123],"dataset":[124],"were":[125,146],"used.":[126],"MetaAll":[127],"was":[128,159,175],"able":[129],"to":[130,194],"identify":[131],"putative":[132],"pathogens":[133],"all":[135],"one":[137],"case.":[138],"case,":[141],"however,":[142],"traditional":[143],"microbiological":[144],"diagnostics":[145,186],"also":[147],"unsuccessful.":[148],"addition,":[150],"co-infection":[151,165],"Haemophilus":[153],"influenzae":[154],"Human":[156],"rhinovirus":[157],"C54":[158],"detected":[160,176],"case":[162,178,181],"1":[163],"SARS-Cov-2":[167],"Influenza":[169],"A":[170],"virus":[171],"(FluA)":[172],"subtype":[173],"H3N2":[174],"3.":[179],"2,":[182],"which":[184],"conventional":[185],"could":[187],"find":[189],"pathogen,":[191],"mNGS":[192],"pointed":[193],"Klebsiella":[195],"pneumoniae":[196],"suspected":[199],"pathogen.":[200],"Finally,":[201],"study":[203],"demonstrated":[204],"importance":[206],"read":[209],"classification,":[210],"contig":[211],"validation":[212],"targeted":[214],"mapping":[216],"more":[218],"reliable":[219],"infectious":[222],"agents":[223],"metagenome":[226],"samples.":[227]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2024-11-17T00:00:00"}
