Abstract
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.
Highlights
Identifying the kinds of viruses that infect eukaryotes and prokaryotes and understanding their functions are important because they are the most abundant entities on Earth (Paez-Espino et al, 2016)
FastViromeExplorer, written in Java, has two main steps: (1) the read mapping step where all reads are mapped to a reference database, and (2) the filtering step where the mapping results are subjected to three major filters for output of the final results on virus types and abundances
Our results show that FastViromeExplorer can be applied to detect and quantify viruses and phages in metagenomic samples taken from environmental samples, and the results are accurate if given a sufficiently complete reference database
Summary
Identifying the kinds of viruses that infect eukaryotes and prokaryotes (phages) and understanding their functions are important because they are the most abundant entities on Earth (Paez-Espino et al, 2016). In the human body there are estimated to be 100 times more viral particles than eukaryotic cells (Fancello, Raoult & Desnues, 2012). Studies have shown that there are connections between human gut microbiome (viruses and bacteria) and diseases such as inflammatory bowel disease (IBD) and colorectal cancer (Mills et al, 2013; Mirzaei & Maurice, 2017; Hannigan et al, 2017). To better understand and eventually prevent such viral outbreaks, it is critical to have timely identification and annotation of viruses. Viruses have been shown to play important roles in shaping the composition and function of environmental microbiomes (Rohwer & Thurber, 2009).
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