{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:43Z","timestamp":1772138023303,"version":"3.50.1"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,12,4]],"date-time":"2023-12-04T00:00:00Z","timestamp":1701648000000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32370700"],"award-info":[{"award-number":["32370700"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170651"],"award-info":[{"award-number":["32170651"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Key Plan for Scientific Research and Development of China","award":["2022YFC2303802"],"award-info":[{"award-number":["2022YFC2303802"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Identification of viruses and further assembly of viral genomes from the next-generation-sequencing data are essential steps in virome studies. This study presented a one-stop tool named VIGA (available at https:\/\/github.com\/viralInformatics\/VIGA) for eukaryotic virus identification and genome assembly from NGS data. It was composed of four modules, namely, identification, taxonomic annotation, assembly and novel virus discovery, which integrated several third-party tools such as BLAST, Trinity, MetaCompass and RagTag. Evaluation on multiple simulated and real virome datasets showed that VIGA assembled more complete virus genomes than its competitors on both the metatranscriptomic and metagenomic data and performed well in assembling virus genomes at the strain level. Finally, VIGA was used to investigate the virome in metatranscriptomic data from the Human Microbiome Project and revealed different composition and positive rate of viromes in diseases of prediabetes, Crohn\u2019s disease and ulcerative colitis. Overall, VIGA would help much in identification and characterization of viromes, especially the known viruses, in future studies.<\/jats:p>","DOI":"10.1093\/bib\/bbad444","type":"journal-article","created":{"date-parts":[[2023,11,14]],"date-time":"2023-11-14T18:16:05Z","timestamp":1699985765000},"source":"Crossref","is-referenced-by-count":5,"title":["VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data"],"prefix":"10.1093","volume":"25","author":[{"given":"Ping","family":"Fu","sequence":"first","affiliation":[{"name":"Hunan University Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, , Changsha 410082, China"}]},{"given":"Yifan","family":"Wu","sequence":"additional","affiliation":[{"name":"Hunan University Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, , Changsha 410082, China"}]},{"given":"Zhiyuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Hunan University Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, , Changsha 410082, China"}]},{"given":"Ye","family":"Qiu","sequence":"additional","affiliation":[{"name":"Hunan University Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, , Changsha 410082, China"}]},{"given":"Yirong","family":"Wang","sequence":"additional","affiliation":[{"name":"Hunan University Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, , Changsha 410082, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5482-9506","authenticated-orcid":false,"given":"Yousong","family":"Peng","sequence":"additional","affiliation":[{"name":"Hunan University Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, , Changsha 410082, 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