{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T08:55:03Z","timestamp":1791881703229,"version":"4.3.4"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:00:00Z","timestamp":1791849600000},"content-version":"vor","delay-in-days":15,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["272983813"],"award-info":[{"award-number":["272983813"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Germany\u2019s Excellence Strategy\u2014EXC 2155\u2014","award":["390874280"],"award-info":[{"award-number":["390874280"]}]},{"name":"Helmholtz Association\u2019s Initiative and Network Fund","award":["398066876\/GRK 2485\/2"],"award-info":[{"award-number":["398066876\/GRK 2485\/2"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>We present Virushunter and Virusgatherer, a bipartite computational workflow for discovering viral genomes from unprocessed next-generation sequencing data. Virushunter conducts a profile Hidden Markov Model-based sequence homology search for viral hallmark protein-coding sequence reads to construct microcontigs, which are used as seeds for targeted viral genome assembly by Virusgatherer. We showcase the application of Virushunter and Virusgatherer through an RNA virus-wide screen in 3348 bat transcriptome sequencing experiments from the Sequence Read Archive. Many of the discovered viruses are likely prototypes of new putative virus species, including a novel alphacoronavirus identified in a South American velvety free-tailed bat and a novel rhabdovirus in a European barbastelle bat. The tools are implemented as a reproducible Snakemake pipeline, which is available at https:\/\/github.com\/lauberlab\/VirusHunterGatherer.<\/jats:p>","DOI":"10.1093\/nargab\/lqag120","type":"journal-article","created":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T12:25:40Z","timestamp":1790425540000},"source":"Crossref","is-referenced-by-count":0,"title":["Data-Driven Virus Discovery with Virushunter and Virusgatherer"],"prefix":"10.1093","volume":"8","author":[{"given":"Liubov","family":"Chuprikova","sequence":"first","affiliation":[{"name":"Division of Virus-Associated Carcinogenesis (D430), German Cancer Research Center (DKFZ) , 69120 Heidelberg ,","place":["Germany"]},{"name":"Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg University , 69117 Heidelberg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li Chuin","family":"Chong","sequence":"additional","affiliation":[{"name":"Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI) , 30625 Hannover ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergej","family":"Ruff","sequence":"additional","affiliation":[{"name":"Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI) , 30625 Hannover ,","place":["Germany"]},{"name":"Institute of Animal Genomics, University of Veterinary Medicine Hannover , 30559 Hannover ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Seitz","sequence":"additional","affiliation":[{"name":"Division of Virus-Associated Carcinogenesis (D430), German Cancer Research Center (DKFZ) , 69120 Heidelberg ,","place":["Germany"]},{"name":"Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg University , 69117 Heidelberg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2265-2953","authenticated-orcid":false,"given":"Chris","family":"Lauber","sequence":"additional","affiliation":[{"name":"Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI) , 30625 Hannover ,","place":["Germany"]},{"name":"Cluster of Excellence 2155 RESIST, Hannover Medical School , 30625 Hannover 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