FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data

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dc.contributor.authorTithi, Saima Sultanaen
dc.contributor.authorAylward, Frank O.en
dc.contributor.authorJensen, Roderick V.en
dc.contributor.authorZhang, Liqingen
dc.contributor.departmentBiological Sciencesen
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2018-01-23T14:33:51Zen
dc.date.available2018-01-23T14:33:51Zen
dc.date.issued2018-01-12en
dc.description.abstractWith the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.en
dc.identifier.doihttps://doi.org/10.7717/peerj.4227en
dc.identifier.pmid29340239en
dc.identifier.urihttp://hdl.handle.net/10919/81898en
dc.identifier.volume6en
dc.language.isoen_USen
dc.publisherPeerJen
dc.rightsCreative Commons Attribution 3.0 United Statesen
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/us/en
dc.subjectMetagenomicsen
dc.subjectViral metagenomicsen
dc.subjectVirusen
dc.subjectPhageen
dc.subjectReference-based virus detectionen
dc.subjectAbundance quantificationen
dc.titleFastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics dataen
dc.title.alternativeFast Virome Exploreren
dc.title.serialPeerJen
dc.typeArticle - Refereeden

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