FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data
With 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 fo...
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doaj-43f40a1bc6f94626abb6798e12780dc72020-11-24T22:38:40ZengPeerJ Inc.PeerJ2167-83592018-01-016e422710.7717/peerj.4227FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics dataSaima Sultana Tithi0Frank O. Aylward1Roderick V. Jensen2Liqing Zhang3Department of Computer Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of AmericaDepartment of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of AmericaDepartment of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of AmericaDepartment of Computer Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of AmericaWith 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.https://peerj.com/articles/4227.pdfMetagenomicsViral metagenomicsVirusPhageReference-based virus detectionAbundance quantification |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Saima Sultana Tithi Frank O. Aylward Roderick V. Jensen Liqing Zhang |
spellingShingle |
Saima Sultana Tithi Frank O. Aylward Roderick V. Jensen Liqing Zhang FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data PeerJ Metagenomics Viral metagenomics Virus Phage Reference-based virus detection Abundance quantification |
author_facet |
Saima Sultana Tithi Frank O. Aylward Roderick V. Jensen Liqing Zhang |
author_sort |
Saima Sultana Tithi |
title |
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data |
title_short |
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data |
title_full |
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data |
title_fullStr |
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data |
title_full_unstemmed |
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data |
title_sort |
fastviromeexplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data |
publisher |
PeerJ Inc. |
series |
PeerJ |
issn |
2167-8359 |
publishDate |
2018-01-01 |
description |
With 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. |
topic |
Metagenomics Viral metagenomics Virus Phage Reference-based virus detection Abundance quantification |
url |
https://peerj.com/articles/4227.pdf |
work_keys_str_mv |
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