{"id":"https://openalex.org/W3184568031","doi":"https://doi.org/10.1186/s12859-021-04294-2","title":"HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences","display_name":"HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences","publication_year":2021,"publication_date":"2021-07-17","ids":{"openalex":"https://openalex.org/W3184568031","doi":"https://doi.org/10.1186/s12859-021-04294-2","mag":"3184568031","pmid":"https://pubmed.ncbi.nlm.nih.gov/34273961"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04294-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04294-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04294-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04294-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039643039","display_name":"Phuoc Truong Nguyen","orcid":"https://orcid.org/0000-0002-4830-4113"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Phuoc Thien Truong Nguyen","raw_affiliation_strings":["Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. phuoc.truong@helsinki.fi","Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland"],"raw_orcid":"https://orcid.org/0000-0002-4830-4113","affiliations":[{"raw_affiliation_string":"Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. phuoc.truong@helsinki.fi","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113158431","display_name":"Ilya Plyusnin","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Ilya Plyusnin","raw_affiliation_strings":["Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland","Institute of Biotechnology, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Institute of Biotechnology, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052281689","display_name":"Tarja Sironen","orcid":"https://orcid.org/0000-0002-2344-2755"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Tarja Sironen","raw_affiliation_strings":["Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland","Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023869007","display_name":"Olli Vapalahti","orcid":"https://orcid.org/0000-0003-2270-6824"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I2800394112","display_name":"Helsinki University Hospital","ror":"https://ror.org/02e8hzf44","country_code":"FI","type":"healthcare","lineage":["https://openalex.org/I2800394112","https://openalex.org/I4210166427"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Olli Vapalahti","raw_affiliation_strings":["Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland","Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland","Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I2800394112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100716048","display_name":"Ravi Kant","orcid":"https://orcid.org/0000-0003-3878-9775"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Ravi Kant","raw_affiliation_strings":["Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland","Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028956140","display_name":"Teemu Smura","orcid":"https://orcid.org/0000-0002-9187-3151"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I2800394112","display_name":"Helsinki University Hospital","ror":"https://ror.org/02e8hzf44","country_code":"FI","type":"healthcare","lineage":["https://openalex.org/I2800394112","https://openalex.org/I4210166427"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Teemu Smura","raw_affiliation_strings":["Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland","Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I2800394112"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5039643039"],"corresponding_institution_ids":["https://openalex.org/I133731052"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":2535,"currency":"EUR","value_usd":2733},"fwci":2.577,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.91694155,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":"22","issue":"1","first_page":"373","last_page":"373"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9017000198364258,"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"}},"topics":[{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9017000198364258,"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/T11754","display_name":"SARS-CoV-2 detection and testing","score":0.025100000202655792,"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":0.019600000232458115,"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/computational-biology","display_name":"Computational biology","score":0.5898319482803345},{"id":"https://openalex.org/keywords/severe-acute-respiratory-syndrome-coronavirus-2","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","score":0.5869675278663635},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5805894136428833},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.5526156425476074},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5008373260498047},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.46440625190734863},{"id":"https://openalex.org/keywords/2019-20-coronavirus-outbreak","display_name":"2019-20 coronavirus outbreak","score":0.4414505362510681},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.4272818863391876},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.404715359210968},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.33391714096069336},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.2725636959075928},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17343729734420776},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1524210274219513},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10091137886047363},{"id":"https://openalex.org/keywords/infectious-disease","display_name":"Infectious disease (medical specialty)","score":0.09364631772041321}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5898319482803345},{"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":0.5869675278663635},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5805894136428833},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.5526156425476074},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5008373260498047},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.46440625190734863},{"id":"https://openalex.org/C3006700255","wikidata":"https://www.wikidata.org/wiki/Q81068910","display_name":"2019-20 coronavirus outbreak","level":3,"score":0.4414505362510681},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.4272818863391876},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.404715359210968},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33391714096069336},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.2725636959075928},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17343729734420776},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1524210274219513},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10091137886047363},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.09364631772041321},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C116675565","wikidata":"https://www.wikidata.org/wiki/Q3241045","display_name":"Outbreak","level":2,"score":0.0},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001938","descriptor_name":"Brazil","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001938","descriptor_name":"Brazil","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001938","descriptor_name":"Brazil","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-021-04294-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04294-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04294-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34273961","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34273961","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:helda.helsinki.fi:10138/332872","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/332872","pdf_url":"http://hdl.handle.net/10138/332872","source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:63ea369fde474f9e8a7434ccfcbb47e0","is_oa":true,"landing_page_url":"https://doaj.org/article/63ea369fde474f9e8a7434ccfcbb47e0","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-8 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8285700","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8285700","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04294-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04294-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04294-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G2583336430","display_name":"Versatile Emerging infectious disease Observatory","funder_award_id":"874735","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5565683214","display_name":null,"funder_award_id":"874735","funder_id":"https://openalex.org/F4320322282","funder_display_name":"Jane ja Aatos Erkon S\u00e4\u00e4ti\u00f6"},{"id":"https://openalex.org/G5660528822","display_name":null,"funder_award_id":"336490","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G7486884968","display_name":"Inhibitors of SARS-Coronavirus-2 infection","funder_award_id":"336490","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G8689965570","display_name":null,"funder_award_id":"874735","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G8863602888","display_name":null,"funder_award_id":"874735","funder_id":"https://openalex.org/F4320335254","funder_display_name":"Horizon 2020"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320322282","display_name":"Jane ja Aatos Erkon S\u00e4\u00e4ti\u00f6","ror":"https://ror.org/03vxy9y38"},{"id":"https://openalex.org/F4320335254","display_name":"Horizon 2020","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3184568031.pdf","grobid_xml":"https://content.openalex.org/works/W3184568031.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1964807436","https://openalex.org/W2007218683","https://openalex.org/W2095680943","https://openalex.org/W2102619694","https://openalex.org/W2103685216","https://openalex.org/W2108234281","https://openalex.org/W2128505445","https://openalex.org/W2130203599","https://openalex.org/W2131271579","https://openalex.org/W2170551349","https://openalex.org/W2412774630","https://openalex.org/W2514298796","https://openalex.org/W2587970647","https://openalex.org/W2605343262","https://openalex.org/W2951912016","https://openalex.org/W2952045272","https://openalex.org/W3043124965","https://openalex.org/W3048531412","https://openalex.org/W3116015992","https://openalex.org/W3120079728","https://openalex.org/W3123500074","https://openalex.org/W3127353402","https://openalex.org/W3180301457","https://openalex.org/W4210756053","https://openalex.org/W6715151218"],"related_works":["https://openalex.org/W3127156785","https://openalex.org/W3009669391","https://openalex.org/W4200329650","https://openalex.org/W4205215807","https://openalex.org/W3005417802","https://openalex.org/W4205754011","https://openalex.org/W4226296940","https://openalex.org/W3028835529","https://openalex.org/W3036314732","https://openalex.org/W3134376730"],"abstract_inverted_index":{"BACKGROUND:":[0],"SARS-CoV-2":[1,16,51,97,139,160,184,203],"related":[2],"research":[3],"has":[4],"increased":[5],"in":[6,50,99,196],"importance":[7],"worldwide":[8],"since":[9],"December":[10],"2019.":[11],"Several":[12],"new":[13],"variants":[14,47,106,185],"of":[15,20,85,107,124,183,186,202],"have":[17,110],"emerged":[18],"globally,":[19],"which":[21,89],"the":[22,29,33,39,83,135,181,200],"most":[23],"notable":[24],"and":[25,38,44,62,133,174,179,208,215],"concerning":[26],"currently":[27,193],"are":[28,55,211],"UK":[30],"variant":[31,36,41],"B.1.1.7,":[32],"South":[34],"African":[35],"B1.351":[37],"Brazilian":[40],"P.1.":[42],"Detecting":[43],"monitoring":[45,199],"novel":[46],"is":[48,70,143,164,192],"essential":[49],"surveillance.":[52],"While":[53],"there":[54],"several":[56,147],"tools":[57,149],"for":[58,122,155,167,198],"assembling":[59],"virus":[60],"genomes":[61],"performing":[63,73],"lineage":[64],"analyses":[65,154],"to":[66,72,82,101,104,138,150,177],"investigate":[67],"SARS-CoV-2,":[68],"each":[69],"limited":[71],"singular":[74],"or":[75],"a":[76,144,171],"few":[77],"functions":[78],"separately.":[79],"RESULTS:":[80],"Due":[81],"lack":[84],"publicly":[86],"available":[87,212],"pipelines,":[88],"could":[90],"perform":[91,151],"fast":[92,175],"reference-based":[93],"assemblies":[94],"on":[95],"raw":[96,130],"sequences":[98],"addition":[100],"identifying":[102],"lineages":[103,137],"detect":[105,178],"concern,":[108],"we":[109],"developed":[111],"an":[112],"open":[113],"source":[114,209],"bioinformatic":[115,148],"pipeline":[116,145,163],"called":[117],"HAVoC":[118,126,142,191,205],"(Helsinki":[119],"university":[120],"Analyzer":[121],"Variants":[123],"Concern).":[125],"can":[127],"reference":[128],"assemble":[129],"sequence":[131],"reads":[132],"assign":[134],"corresponding":[136],"sequences.":[140],"CONCLUSIONS:":[141],"utilizing":[146],"multiple":[152],"necessary":[153],"investigating":[156],"genetic":[157],"variance":[158],"among":[159],"samples.":[161],"The":[162],"particularly":[165],"useful":[166],"those":[168],"who":[169],"need":[170],"more":[172],"accessible":[173],"tool":[176],"monitor":[180],"spread":[182,201],"concern":[187],"during":[188],"local":[189],"outbreaks.":[190],"being":[194],"used":[195],"Finland":[197],"variants.":[204],"user":[206],"manual":[207],"code":[210],"at":[213],"https://www.helsinki.fi/en/projects/havoc":[214],"https://bitbucket.org/auto_cov_pipeline/havoc":[216],",":[217],"respectively.":[218]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
