ViralRecall—A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in ‘Omic Data

Abstract

Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs are frequently abundant in metagenomic datasets, and that sequences derived from these viruses can also be found endogenized in diverse eukaryotic genomes. The accurate detection of sequences derived from NCLDVs is therefore of great importance, but this task is challenging owing to both the high level of sequence divergence between NCLDV families and the extraordinarily high diversity of genes encoded in their genomes, including some encoding for metabolic or translation-related functions that are typically found only in cellular lineages. Here, we present ViralRecall, a bioinformatic tool for the identification of NCLDV signatures in ‘omic data. This tool leverages a library of giant virus orthologous groups (GVOGs) to identify sequences that bear signatures of NCLDVs. We demonstrate that this tool can effectively identify NCLDV sequences with high sensitivity and specificity. Moreover, we show that it can be useful both for removing contaminating sequences in metagenome-assembled viral genomes as well as the identification of eukaryotic genomic loci that derived from NCLDV. ViralRecall is written in Python 3.5 and is freely available on GitHub: https://github.com/faylward/viralrecall.

A phylogenomic framework for charting the diversity and evolution of giant viruses

“…From each cluster, we chose the genome with the highest N50 contig length as the representative. We then decontaminated the genomes through analysis with ViralRecall v.2.0 [62] (-c parameter), with all contigs with negative scores removed on the grounds that they represent non-Nucleocytoviricota contamination or highly unusual gene composition that cannot be validated by our present knowledge of Nucleocytoviricota genomic content. We only considered contigs >10 kbp, given the inherent difficulty in eliminating contamination derived from short contigs.…”

A Phylogenomic Framework for Charting the Diversity and Evolution of Giant Viruses

“…From each cluster, we chose the genome with the highest N50 contig length as the representative. We then decontaminated the genomes through analysis with ViralRecall v.2.0 [52] (-c parameter), with all contigs with negative scores removed on the grounds that they represent non-Nucleocytoviricota contamination or highly unusual gene composition that cannot be validated by our present knowledge of Nucleocytoviricota genomic content. We only considered contigs > 10 kbp given the inherent difficulty in eliminating contamination derived from short contigs.…”

Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae

“…For this study, we analyzed 35 Asfarvirus MAGs generated in two previous studies (Moniruzzaman et al, 2020a;Schulz et al, 2020) and complete genomes of five Asfarviruses (Reteno et al, 2015;Silva et al, 2015;Bajrai et al, 2016;Andreani et al, 2017;Matsuyama et al, 2020). MAGs were quality-checked using ViralRecall v. 2.0 (default parameters), with results manually inspected to ensure that no large non-NCLDV contigs were present (Aylward and Moniruzzaman, 2021). We used Seqkit v0.12.0 (Shen et al, 2016) for FASTA/Q file manipulation to generate the statistics of the genomes and proteins.…”