ArticleNucleic acids research2022
vRhyme enables binning of viral genomes from metagenomes.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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Who cites it
80 citing papers in PubMed.
- Distinct Evolutionary Selection Patterns in Temperate and Filamentous Phages of Phocaeicola vulgatus in Health and IBD.Research square · 2026Article
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- Adaptation of Soil Viruses to Salinity Stress: Insights Into Genome Size Expansion and Functional Diversification.Environmental microbiology · 2026Article
- A genomic catalog of the mouse gut virome reveals features associated with ageing.Nature communications · 2026Article
- Bacteriophage replication strategies are associated with organic matter energy content on coral reefs.mSystems · 2026Article
- VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion.Bioinformatics (Oxford, England) · 2026Article
- A diverse gut virome in natural populations of Drosophila melanogaster.Animal microbiome · 2026Article
- Ten quick tips for classifying unknown bacteriophage.PLoS computational biology · 2026Article
- Article
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- The human skin virome: Ecological dynamics, aberrant profiles, and therapeutic opportunities.Cell host & microbe · 2026Review
- nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction.Bioinformatics (Oxford, England) · 2026Article
- Annual Dynamics and Functional Traits of Viral Communities in Tropical Intertidal Sands of Sanya Bay.Viruses · 2026Article
- Microbial decomposer diversity and metabolic function during the decomposition of brine shrimp carcasses in a saline lake.Microbiome · 2026Article
- Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.NPJ biofilms and microbiomes · 2026Article
- Impact of phage enrichment on the observed infant gut phageome.Microbiology spectrum · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.Nature communications · 2026Article
- Ultra-deep metagenomic sequencing enables reconstruction of diverse, high quality microbial genomes from human urine samples.BMC microbiology · 2026Article
- Unraveling the Coevolutionary Dynamics of Phage and Bacterial Protein Warfare Occurring in the Drains of Beef-Processing Plants.Microorganisms · 2026Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs supervised machine learning to identify nucleotide feature similarities, which are compiled into iterations of weighted networks and refined bins. To refine bins, vRhyme utilizes unique features of viral genomes, namely a protein redundancy scoring mechanism based on the observation that viruses seldom encode redundant genes. Using simulated viromes, we displayed superior performance of vRhyme compared to available binning tools in constructing more complete and uncontaminated vMAGs. When applied to 10,601 viral scaffolds from human skin, vRhyme advanced our understanding of resident viruses, highlighted by identification of a Herelleviridae vMAG comprised of 22 scaffolds, and another vMAG encoding a nitrate reductase metabolic gene, representing near-complete genomes post-binning. vRhyme will enable a convention of binning uncultivated viral genomes and has the potential to transform metagenome-based viral ecology.
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