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However, these methods can introduce virus sequence contaminations into viral genomes when short, fragmented partial sequences are present in the assembled contigs. These contaminations can lead to incorrect analyses;\u00a0however, practical detection tools are lacking. In this study, we introduce vClean, a novel automated tool that detects contaminations in viral genomes. By applying machine learning to the nucleotide sequence features and gene patterns of the input viral genome, vClean could identify contaminations. Specifically, for tailed double-stranded DNA phages, we attempted accurate predictions by defining single-copy-like genes and counting their duplications. We evaluated the performance of vClean using\u00a0simulated datasets derived from complete reference genomes, achieving a binary accuracy of 0.932. When vClean was applied to 4693 genomes of medium or higher quality derived from public ocean metagenomic data, 1604 genomes (34.2%) were identified as contaminated. We also demonstrated that vClean can detect contamination in single-virus genome data obtained from river water. vClean provides a new benchmark for quality control of environmental viral genomes and has the potential to become an essential tool for environmental viral genome analysis.<\/jats:p>","DOI":"10.1093\/nargab\/lqae185","type":"journal-article","created":{"date-parts":[[2024,12,18]],"date-time":"2024-12-18T23:30:05Z","timestamp":1734564605000},"source":"Crossref","is-referenced-by-count":4,"title":["vClean: assessing virus sequence contamination in viral genomes"],"prefix":"10.1093","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5400-7521","authenticated-orcid":false,"given":"Ryota","family":"Wagatsuma","sequence":"first","affiliation":[{"name":"Department of Life Science and Medical Bioscience,\u00a0Graduate School of Advanced Science and Engineering, Waseda University , 2-2 Wakamatsu-cho , Shinjuku-ku , Tokyo\u00a0 162-8480 ,","place":["Japan"]},{"name":"Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University , 3-4-1 Okubo , Shinjuku-ku , Tokyo\u00a0 169-0072 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5443-7230","authenticated-orcid":false,"given":"Yohei","family":"Nishikawa","sequence":"additional","affiliation":[{"name":"Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University , 3-4-1 Okubo , Shinjuku-ku , Tokyo\u00a0 169-0072 ,","place":["Japan"]},{"name":"Research Organization for Nano & Life Innovation, Waseda University , 513 Waseda Tsurumaki-cho , Shinjuku-ku , Tokyo\u00a0 162-0041 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7070-4690","authenticated-orcid":false,"given":"Masahito","family":"Hosokawa","sequence":"additional","affiliation":[{"name":"Department of Life Science and Medical Bioscience,\u00a0Graduate School of Advanced Science and Engineering, Waseda University , 2-2 Wakamatsu-cho , Shinjuku-ku , Tokyo\u00a0 162-8480 ,","place":["Japan"]},{"name":"Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University , 3-4-1 Okubo , Shinjuku-ku , Tokyo\u00a0 169-0072 ,","place":["Japan"]},{"name":"Research Organization for Nano & Life Innovation, Waseda University , 513 Waseda Tsurumaki-cho , Shinjuku-ku , Tokyo\u00a0 162-0041 ,","place":["Japan"]},{"name":"Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University , 3-4-1 Okubo , Shinjuku-ku , Tokyo\u00a0 169-8555 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haruko","family":"Takeyama","sequence":"additional","affiliation":[{"name":"Department of Life Science and Medical Bioscience,\u00a0Graduate School of Advanced Science and Engineering, Waseda University , 2-2 Wakamatsu-cho , Shinjuku-ku , Tokyo\u00a0 162-8480 ,","place":["Japan"]},{"name":"Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University , 3-4-1 Okubo , Shinjuku-ku , Tokyo\u00a0 169-0072 ,","place":["Japan"]},{"name":"Research Organization for Nano & Life Innovation, Waseda University , 513 Waseda Tsurumaki-cho , Shinjuku-ku , Tokyo\u00a0 162-0041 ,","place":["Japan"]},{"name":"Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University , 3-4-1 Okubo , Shinjuku-ku , Tokyo\u00a0 169-8555 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,7]]},"reference":[{"key":"2025030419180691100_B1","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1038\/340467a0","article-title":"High abundance of viruses found in aquatic environments","volume":"340","author":"Bergh","year":"1989","journal-title":"Nature"},{"key":"2025030419180691100_B2","doi-asserted-by":"crossref","first-page":"e00052-20","DOI":"10.1128\/JB.00052-20","article-title":"Are there 1031 virus particles on Earth, or more, or fewer?","volume":"202","author":"Mushegian","year":"2020","journal-title":"J. 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