iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

Abstract

Microbes affect nutrient and energy transformations throughout the world's ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps') for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infectArchaeaandBacteria

“…Further, we make these approaches accessible to researchers by developing a tool, vConTACT (Viral CONTigs Automatic Clustering and Taxonomy), and deploy it as part of the iVirus ecosystem of apps that leverages the CyVerse cyberinfrastructure (Bolduc et al, 2016). …”

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

“…Furthermore, metadata such as isolation source or habitat where the virus was originally identified, or information about its putative host, often remains elusive or not available in several of these databases. More recent works are making a great progress towards an effort to provide a centralized resource for viral data and associated tools (19). However, despite the excellent existing resources, we still lack a data management and visualization environment integrating viral genes, genomes, clusters, functions, associated host and habitat with analytical tools that would enable large-scale comparative analysis of the global virome.…”

Virus taxonomy in the age of metagenomics

“…Furthermore, numerous viruses are hidden in publicly available microbial genomic datasets. A recently developed tool, VirSorter 37,38 , identified 12,498 new viral genome sequences in ~15,000 bacterial and archaeal genomes 37 , which increased the number of known prokaryotic viruses ~10-fold and identified viruses that infect 13 prokaryotic phyla 37,38 . These advances are a striking testimony to the fundamental change in virus discovery: the overwhelming majority of new viral genomes now come from metagenomic data and have never been directly linked to biological agents.…”