{"id":"https://openalex.org/W4414346805","doi":"https://doi.org/10.1093/bioinformatics/btaf516","title":"Misdetection of frameshifts in SARS-CoV-2 genomes: need for additional harmonisation and efficient monitoring of data workflows","display_name":"Misdetection of frameshifts in SARS-CoV-2 genomes: need for additional harmonisation and efficient monitoring of data workflows","publication_year":2025,"publication_date":"2025-09-12","ids":{"openalex":"https://openalex.org/W4414346805","doi":"https://doi.org/10.1093/bioinformatics/btaf516","pmid":"https://pubmed.ncbi.nlm.nih.gov/40971804"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf516","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf516","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf516/64273371/btaf516.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/btaf516/64273371/btaf516.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Rok Kogoj","raw_affiliation_strings":["Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana , Ljubljana,","Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia"],"affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana , Ljubljana,","institution_ids":["https://openalex.org/I153976015"]},{"raw_affiliation_string":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"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/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 20129,","Seidor Italy S.r.l, Milan 20129, Italy"],"affiliations":[{"raw_affiliation_string":"Seidor Italy S.r.l. , Milan 20129,","institution_ids":["https://openalex.org/I4210166283"]},{"raw_affiliation_string":"Seidor Italy S.r.l, Milan 20129, Italy","institution_ids":[]}]},{"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"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Samo Zakotnik","raw_affiliation_strings":["Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana , Ljubljana,","Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia"],"affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana , Ljubljana,","institution_ids":["https://openalex.org/I153976015"]},{"raw_affiliation_string":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia","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"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Alen Sulji\u010d","raw_affiliation_strings":["Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana , Ljubljana,","Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia"],"affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana , Ljubljana,","institution_ids":["https://openalex.org/I153976015"]},{"raw_affiliation_string":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","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"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Mi\u0161a Korva","raw_affiliation_strings":["Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana , Ljubljana,","Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia"],"affiliations":[{"raw_affiliation_string":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana , Ljubljana,","institution_ids":["https://openalex.org/I153976015"]},{"raw_affiliation_string":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"last","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":"funder","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"]}],"countries":["BE","IT"],"is_corresponding":false,"raw_author_name":"Gabriele Leoni","raw_affiliation_strings":["European Commission, Joint Research Centre (JRC) , Ispra,","European Commission, Joint Research Centre (JRC), Ispra, Italy"],"affiliations":[{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC) , Ispra,","institution_ids":["https://openalex.org/I2800387288"]},{"raw_affiliation_string":"European Commission, Joint Research Centre (JRC), Ispra, Italy","institution_ids":["https://openalex.org/I4210118689"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5056379783"],"corresponding_institution_ids":["https://openalex.org/I153976015"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.31565126,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9915000200271606,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9901999831199646,"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":0.8256999850273132},{"id":"https://openalex.org/keywords/turnaround-time","display_name":"Turnaround time","score":0.6284000277519226},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.597599983215332},{"id":"https://openalex.org/keywords/frameshift-mutation","display_name":"Frameshift mutation","score":0.49399998784065247},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4180000126361847},{"id":"https://openalex.org/keywords/pandemic","display_name":"Pandemic","score":0.3928999900817871},{"id":"https://openalex.org/keywords/severe-acute-respiratory-syndrome-coronavirus-2","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","score":0.383899986743927},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.361299991607666}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8256999850273132},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6473000049591064},{"id":"https://openalex.org/C176553487","wikidata":"https://www.wikidata.org/wiki/Q7855819","display_name":"Turnaround time","level":2,"score":0.6284000277519226},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.597599983215332},{"id":"https://openalex.org/C29906990","wikidata":"https://www.wikidata.org/wiki/Q1440688","display_name":"Frameshift mutation","level":4,"score":0.49399998784065247},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4180000126361847},{"id":"https://openalex.org/C89623803","wikidata":"https://www.wikidata.org/wiki/Q12184","display_name":"Pandemic","level":5,"score":0.3928999900817871},{"id":"https://openalex.org/C3007834351","wikidata":"https://www.wikidata.org/wiki/Q82069695","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","level":5,"score":0.383899986743927},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3785000145435333},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.362199991941452},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.361299991607666},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3449999988079071},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3391999900341034},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33329999446868896},{"id":"https://openalex.org/C2779927696","wikidata":"https://www.wikidata.org/wiki/Q6865654","display_name":"Minion","level":5,"score":0.3248000144958496},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.3163999915122986},{"id":"https://openalex.org/C3006700255","wikidata":"https://www.wikidata.org/wiki/Q81068910","display_name":"2019-20 coronavirus outbreak","level":3,"score":0.3086000084877014},{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.2775000035762787},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.2578999996185303},{"id":"https://openalex.org/C126042441","wikidata":"https://www.wikidata.org/wiki/Q1324888","display_name":"Frame (networking)","level":2,"score":0.2500999867916107}],"mesh":[{"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":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","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":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","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":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018965","descriptor_name":"Frameshifting, Ribosomal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018965","descriptor_name":"Frameshifting, Ribosomal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018965","descriptor_name":"Frameshifting, Ribosomal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018965","descriptor_name":"Frameshifting, Ribosomal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018965","descriptor_name":"Frameshifting, Ribosomal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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":false},{"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":false},{"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf516","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf516","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf516/64273371/btaf516.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:40971804","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40971804","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:11363368","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12557093","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf516","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf516","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf516/64273371/btaf516.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":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320330608","display_name":"Ministrstvo za zdravje","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414346805.pdf","grobid_xml":"https://content.openalex.org/works/W4414346805.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W2605343262","https://openalex.org/W2605897695","https://openalex.org/W2765185461","https://openalex.org/W3043272866","https://openalex.org/W3135383916","https://openalex.org/W3135409471","https://openalex.org/W3180925673","https://openalex.org/W4206499307","https://openalex.org/W4285498614","https://openalex.org/W4296231452","https://openalex.org/W4313880130","https://openalex.org/W4315651561","https://openalex.org/W4320879640","https://openalex.org/W4389234745","https://openalex.org/W4398182689","https://openalex.org/W4408170149"],"related_works":[],"abstract_inverted_index":{"Five":[0],"years":[1],"after":[2],"the":[3,6,46,63,83,98,163,177,184,197,203,219],"outbreak":[4],"of":[5,18,20,25,36,85,132,139,158,166,174,202,225],"SARS-CoV-2":[7,26,43],"pandemic":[8],"in":[9,122,146,162,176],"2020,":[10],"diagnostic":[11],"laboratories":[12,88],"have":[13,70,109],"moved":[14],"from":[15],"massive":[16],"sequencing":[17,94],"thousands":[19],"samples":[21,86],"to":[22,39,51,73,118,150,170,186],"routine":[23],"surveillance":[24],"cases,":[27],"as":[28,45],"with":[29,183],"all":[30],"other":[31],"respiratory":[32],"viruses.":[33],"Surveillance":[34],"remains":[35],"paramount":[37],"importance":[38],"prevent":[40],"a":[41,123,136,144,156],"further":[42],"surge,":[44],"virus":[47],"has":[48],"been":[49,71],"shown":[50],"mutate":[52],"rapidly":[53],"and":[54,59,68,79,96,113,179,214,217,228],"can":[55,116,206],"render":[56],"available":[57],"drugs":[58],"vaccines":[60],"ineffective.":[61],"During":[62],"pandemic,":[64],"several":[65],"bioinformatics":[66,124],"pipelines":[67],"workflows":[69,216],"developed":[72],"streamline":[74],"analysis,":[75],"shorten":[76],"turnaround":[77],"time":[78,112,114],"ensure":[80],"reproducibility.":[81],"As":[82],"number":[84],"decreases,":[87],"are":[89,126],"moving":[90],"towards":[91,230],"more":[92,231],"flexible":[93],"strategies":[95],"optimizing":[97],"cost":[99],"per":[100],"sample.":[101],"However,":[102],"workflow":[103],"redesigns,":[104],"even":[105,191,208],"if":[106],"individual":[107],"steps":[108],"proven":[110],"successful":[111],"again,":[115],"lead":[117],"challenges":[119,204],"when":[120,209],"changes":[121],"pipeline":[125],"introduced":[127],"(e.g.":[128],"version":[129],"updates,":[130],"implementation":[131],"new":[133,137],"features,":[134],"etc.),":[135],"combination":[138],"viral":[140,181],"mutations":[141,161,175],"emerge":[142],"or":[143,190],"change":[145],"wet-lab":[147],"procedures":[148],"leads":[149],"unpredictable":[151],"results.":[152],"Here,":[153],"we":[154],"present":[155],"report":[157],"misidentified":[159],"frameshift":[160],"consensus":[164],"sequence":[165],"SARS-CoV-2,":[167],"which":[168],"led":[169],"an":[171],"incorrect":[172],"assumption":[173],"spike":[178],"nucleocapsid":[180],"proteins":[182],"potential":[185],"affect":[187],"PCR":[188],"detection":[189],"antigen":[192],"testing.":[193],"This":[194],"investigation":[195],"exemplifies":[196],"need":[198,220],"for":[199,221],"better":[200],"awareness":[201],"that":[205],"occur":[207],"using":[210],"routinely":[211],"applied":[212],"protocols":[213],"analytical":[215],"highlights":[218],"cooperation":[222],"between":[223],"experts":[224],"NGS,":[226],"bioinformaticians":[227],"decision-makers":[229],"harmonized":[232],"data":[233],"workflows.":[234]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
