{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T09:03:15Z","timestamp":1775811795698,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2020,5,15]],"date-time":"2020-05-15T00:00:00Z","timestamp":1589500800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["19-14-00172"],"award-info":[{"award-number":["19-14-00172"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004285","name":"Saint Petersburg State University","doi-asserted-by":"publisher","award":["51555639"],"award-info":[{"award-number":["51555639"]}],"id":[{"id":"10.13039\/501100004285","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NSF\/MCB-BSF","award":["1715911"],"award-info":[{"award-number":["1715911"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth\u2019s virome has been sequenced so far. Shotgun metagenomic sequencing provides an opportunity to reveal novel viruses but faces the computational challenge of identifying viral genomes that are often difficult to detect in metagenomic assemblies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We describe a MetaviralSPAdes tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked MetaviralSPAdes on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models and demonstrated that it improves on the state-of-the-art viral identification pipelines.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Metaviral SPAdes includes ViralAssembly, ViralVerify and ViralComplete modules that are available as standalone packages: https:\/\/github.com\/ablab\/spades\/tree\/metaviral_publication, https:\/\/github.com\/ablab\/viralVerify\/ and https:\/\/github.com\/ablab\/viralComplete\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>d.antipov@spbu.ru<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa490","type":"journal-article","created":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T19:11:53Z","timestamp":1588965113000},"page":"4126-4129","source":"Crossref","is-referenced-by-count":292,"title":["<scp>Metaviral<\/scp>\n                  <scp>SPAdes<\/scp>: assembly of viruses from metagenomic data"],"prefix":"10.1093","volume":"36","author":[{"given":"Dmitry","family":"Antipov","sequence":"first","affiliation":[{"name":"Institute for Translational Biomedicine, St. Petersburg State University Institute of Translational Biomedicine, Center of Algorithmic Biotechnology, , St. Petersburg 199004, Russia"}]},{"given":"Mikhail","family":"Raiko","sequence":"additional","affiliation":[{"name":"Institute for Translational Biomedicine, St. Petersburg State University Institute of Translational Biomedicine, Center of Algorithmic Biotechnology, , St. Petersburg 199004, Russia"}]},{"given":"Alla","family":"Lapidus","sequence":"additional","affiliation":[{"name":"Institute for Translational Biomedicine, St. Petersburg State University Institute of Translational Biomedicine, Center of Algorithmic Biotechnology, , St. Petersburg 199004, Russia"}]},{"given":"Pavel A","family":"Pevzner","sequence":"additional","affiliation":[{"name":"University of California Department of Computer Science and Engineering, , San Diego, CA 92093-0404, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,5,15]]},"reference":[{"key":"2023062213541664800_btaa490-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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