{"id":"https://openalex.org/W4416098820","doi":"https://doi.org/10.1093/bioinformatics/btaf610","title":"HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements","display_name":"HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements","publication_year":2025,"publication_date":"2025-11-06","ids":{"openalex":"https://openalex.org/W4416098820","doi":"https://doi.org/10.1093/bioinformatics/btaf610","pmid":"https://pubmed.ncbi.nlm.nih.gov/41206760"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf610","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf610","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/12/btaf610/65246986/btaf610.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/article-pdf/41/12/btaf610/65246986/btaf610.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112961894","display_name":"Laura Mu\u00f1oz-Baena","orcid":null},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Laura Mu\u00f1oz-Baena","raw_affiliation_strings":["Department of Biology, University of Oxford , Oxford, OX1 3EL,","Department of Biology, University of Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Oxford , Oxford, OX1 3EL,","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Biology, University of Oxford, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039736122","display_name":"Emma F Harding","orcid":"https://orcid.org/0000-0001-5067-962X"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Emma F Harding","raw_affiliation_strings":["Department of Biology, University of Oxford , Oxford, OX1 3EL,","Department of Biology, University of Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Oxford , Oxford, OX1 3EL,","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Biology, University of Oxford, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084335469","display_name":"Jose Gabriel Nino Barreat","orcid":"https://orcid.org/0000-0002-4589-9473"},"institutions":[{"id":"https://openalex.org/I1336856363","display_name":"Natural History Museum","ror":"https://ror.org/039zvsn29","country_code":"GB","type":"archive","lineage":["https://openalex.org/I1336856363"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jose Gabriel Nino Barreat","raw_affiliation_strings":["Department of Biology, University of Oxford , Oxford, OX1 3EL,","Natural History Museum Life Sciences Department, , London, SW7 5BD,","Department of Biology, University of Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Oxford , Oxford, OX1 3EL,","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Natural History Museum Life Sciences Department, , London, SW7 5BD,","institution_ids":["https://openalex.org/I1336856363"]},{"raw_affiliation_string":"Department of Biology, University of Oxford, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066901530","display_name":"Cormac M. Kinsella","orcid":"https://orcid.org/0000-0001-9865-4608"},"institutions":[{"id":"https://openalex.org/I2801711128","display_name":"Swedish Museum of Natural History","ror":"https://ror.org/05k323c76","country_code":"SE","type":"archive","lineage":["https://openalex.org/I2801711128"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB","SE"],"is_corresponding":false,"raw_author_name":"Cormac M Kinsella","raw_affiliation_strings":["Department of Biology, University of Oxford , Oxford, OX1 3EL,","Swedish Museum of Natural History Department of Bioinformatics and Genetics, , Stockholm, SE-104 05,","Department of Biology, University of Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Oxford , Oxford, OX1 3EL,","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Swedish Museum of Natural History Department of Bioinformatics and Genetics, , Stockholm, SE-104 05,","institution_ids":["https://openalex.org/I2801711128"]},{"raw_affiliation_string":"Department of Biology, University of Oxford, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058450513","display_name":"Aris Katzourakis","orcid":"https://orcid.org/0000-0003-3328-6204"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Aris Katzourakis","raw_affiliation_strings":["Department of Biology, University of Oxford , Oxford, OX1 3EL,","Department of Biology, University of Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Oxford , Oxford, OX1 3EL,","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Biology, University of Oxford, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5112961894"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"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":0.34766907,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11767","display_name":"Poxvirus research and outbreaks","score":0.2842999994754791,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11767","display_name":"Poxvirus research and outbreaks","score":0.2842999994754791,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"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":0.18539999425411224,"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/T10613","display_name":"Virus-based gene therapy research","score":0.05820000171661377,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/pipeline","display_name":"Pipeline (software)","score":0.8828999996185303},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.8410999774932861},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.8241000175476074},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6294000148773193},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5633000135421753},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.506600022315979}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8828999996185303},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8410999774932861},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8241000175476074},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7688999772071838},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6294000148773193},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5633000135421753},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.506600022315979},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.49950000643730164},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4821999967098236},{"id":"https://openalex.org/C2988343187","wikidata":"https://www.wikidata.org/wiki/Q1130645","display_name":"Open source software","level":3,"score":0.42170000076293945},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.375},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3571000099182129},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.3359000086784363},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32179999351501465},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.30880001187324524},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.2928999960422516},{"id":"https://openalex.org/C2777267654","wikidata":"https://www.wikidata.org/wiki/Q3519023","display_name":"Test (biology)","level":2,"score":0.26899999380111694},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.26249998807907104},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.25290000438690186},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.25049999356269836}],"mesh":[{"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":true},{"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":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaf610","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf610","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/12/btaf610/65246986/btaf610.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:41206760","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41206760","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:11516763","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12707981","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"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:9e64a608-c31d-4572-80a1-1a5ccfc97cd8","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Jisc Publications Router","raw_type":"http://purl.org/coar/resource_type/c_dcae04bc"},{"id":"pmh:oai:pubmedcentral.nih.gov:12707981","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12707981/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf610","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf610","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/12/btaf610/65246986/btaf610.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":[{"id":"https://openalex.org/G4155004294","display_name":null,"funder_award_id":"101001623-PALVIREVOL","funder_id":"https://openalex.org/F4320338335","funder_display_name":"H2020 European Research Council"}],"funders":[{"id":"https://openalex.org/F4320320290","display_name":"University of Oxford","ror":"https://ror.org/052gg0110"},{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416098820.pdf"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1971002293","https://openalex.org/W1996423252","https://openalex.org/W2022756574","https://openalex.org/W2039337517","https://openalex.org/W2074897380","https://openalex.org/W2101360032","https://openalex.org/W2102619694","https://openalex.org/W2108787198","https://openalex.org/W2110882852","https://openalex.org/W2114850508","https://openalex.org/W2303521084","https://openalex.org/W2529838505","https://openalex.org/W2605897695","https://openalex.org/W2795297546","https://openalex.org/W3121979517","https://openalex.org/W3143063265","https://openalex.org/W3160148332","https://openalex.org/W3197612411","https://openalex.org/W4205443759","https://openalex.org/W4229015127","https://openalex.org/W4240311092","https://openalex.org/W4246297253","https://openalex.org/W4294253063","https://openalex.org/W4302773998","https://openalex.org/W4307169571","https://openalex.org/W4310651672","https://openalex.org/W4363678132","https://openalex.org/W4393947158","https://openalex.org/W4396870359","https://openalex.org/W4402903656","https://openalex.org/W4403562904","https://openalex.org/W4403619477","https://openalex.org/W4407417568"],"related_works":[],"abstract_inverted_index":{"The":[0,44],"HI-FEVER":[1,59],"source":[2],"code":[3],"is":[4,30],"available":[5,31],"on":[6,20,41,63],"GitHub":[7],"at":[8,25,32],"https://github.com/PaleovirologyLab/hi-fever.":[9],"Minimal":[10],"reference":[11],"databases,":[12],"test":[13],"datasets":[14],"and":[15,39,53,56,68,71],"benchmarking":[16],"results":[17],"are":[18],"hosted":[19],"the":[21],"Open":[22],"Science":[23],"Framework":[24],"https://osf.io/y357r.":[26],"A":[27],"detailed":[28],"wiki":[29],"https://github.com/PaleovirologyLab/hi-fever/wiki,":[33],"including":[34],"usage":[35],"instructions,":[36],"parameter":[37],"descriptions,":[38],"guidance":[40],"interpreting":[42],"outputs.":[43],"pipeline":[45],"includes":[46],"a":[47],"Pixi":[48],"environment":[49],"compatible":[50],"with":[51],"Conda":[52],"Apptainer":[54],"containerization,":[55],"Docker":[57],"images.":[58],"has":[60],"been":[61],"tested":[62],"Linux,":[64],"Windows":[65],"(via":[66],"WSL2),":[67],"macOS":[69],"(Intel":[70],"ARM64).":[72]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-11-10T00:00:00"}
