VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Abstract

Background Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Results Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. Conclusion With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available (https://bitbucket.org/MAVERICLab/virsorter2), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse (https://de.cyverse.org/de).

DNase treatment improves viral enrichment in agricultural soil viromes

“…Analyses of overall assembly statistics (Figure 1) were performed on these data. Putative viral contigs were then identified using VirSorter in decontamination mode, retaining any contigs that were assigned as higher confidence categories (1, 2, 4, or 5), in accordance with established recommendations (10,18,25,28). Analyses considering viral…”

“…The copyright holder for this preprint (which this version posted June 3, 2021. ; https://doi.org/10.1101/2021.06.01.446688 doi: bioRxiv preprint hallmark genes and other viral sequence signatures) (25)(26)(27)(28) and efforts to compile viral reference databases that include partial and putative viral genomes (1,19,29) have improved our ability to recognize viral genomic sequences in soil metagenomes. However, despite these advances, our ability to catalog soil viral diversity is still largely gated by the low prevalence of viral DNA in total soil metagenomes, which tend to be dominated by bacterial and archaeal sequences (10,19,30).…”

The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome

“…Are the genomes assembled phage genomes? De-novo prediction of phages using tools such as VirFinder/ DeepVirFinder (Ren et al 2017;Ren et al, 2002) and VirSorter2 (Guo et al, 2021) Confirmation of viral genome completeness with CheckV (Nayfach et al, 2020) and IMG/VR v3 (Roux et al, 2021). How diverse are the phages?…”

Hundreds of viral families in the healthy infant gut

“…A series of virus discovery and decontamination tools have been published recently 21,37,[49][50][51][52][53][54][55] and they have already seen widespread application by the viromics community for decontaminating viromes and prediction of viral sequences in published metagenomes. Entire databases have been released that were built on predictions from such tools 22,35 , yet little is known about their sensitivities to novel viral clades, or their ability to weed out virome-contaminating DNA.…”