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

PeerJ

article

Saima Sultana Tithi¹  Frank O. Aylward²  Roderick V. Jensen²  Liqing Zhang¹ 

[1] Department of Computer Science, Virginia Polytechnic Institute and State University;Department of Biological Sciences, Virginia Polytechnic Institute and State University

关键词: Metagenomics;    Viral metagenomics;    Virus;    Phage;    Reference-based virus detection;    Abundance quantification;   

DOI  :  10.7717/peerj.4227

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY