ArticleNature protocols2017
Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data.
Article in Nature protocols, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
- Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau.Nature communications · 2026Article
- Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions.Microbiome · 2026Article
- Diversity, transfer potential, and transcriptional activity of virus-carried antibiotic resistance genes in global estuaries.iMetaOmics · 2026Article
- Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.Environmental science and ecotechnology · 2026Article
- Bacteriophages in gut metagenomes: from analysis to application.Virology journal · 2026Review
- Co-detection and genomic characterization of avian rotavirus A, avian orthoreovirus, and chicken megrivirus-C using nontargeted metagenomic surveillance in Indian broiler chickens.Frontiers in cellular and infection microbiology · 2026Article
- Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.Nature communications · 2025Article
- Comprehensive discovery and functional characterization of diverse prophages in the pig gut microbiome.Frontiers in microbiology · 2025Article
- Unveiling the unknown viral world in groundwater.Nature communications · 2024Article
- The effects of sequencing strategies on Metagenomic pathogen detection using bronchoalveolar lavage fluid samples.Heliyon · 2024Article
- Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining.Microbiome · 2024Article
- Hidden diversity and potential ecological function of phosphorus acquisition genes in widespread terrestrial bacteriophages.Nature communications · 2024Article
- The gut ileal mucosal virome is disturbed in patients with Crohn's disease and exacerbates intestinal inflammation in mice.Nature communications · 2024Article
- Macroalgal virosphere assists with host-microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments.The ISME journal · 2024Article
- Soil viral diversity, ecology and climate change.Nature reviews. Microbiology · 2023Review
- Genomic diversity and ecological distribution of marineMarine life science & technology · 2023Article
- Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori.Nature communications · 2023Article
- Viral Community Structure and Potential Functions in the Dried-Out Aral Sea Basin Change along a Desiccation Gradient.mSystems · 2023Article
- IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.Nucleic acids research · 2023Article
- DETIRE: a hybrid deep learning model for identifying viral sequences from metagenomes.Frontiers in microbiology · 2023Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The analysis of large microbiome data sets holds great promise for the delineation of the biological and metabolic functioning of living organisms and their role in the environment. In the midst of this genomic puzzle, viruses, especially those that infect microbial communities, represent a major reservoir of genetic diversity with great impact on biogeochemical cycles and organismal health. Overcoming the limitations associated with virus detection directly from microbiomes can provide key insights into how ecosystem dynamics are modulated. Here, we present a computational protocol for accurate detection and grouping of viral sequences from microbiome samples. Our approach relies on an expanded and curated set of viral protein families used as bait to identify viral sequences directly from metagenomic assemblies. This protocol describes how to use the viral protein families catalog (∼7 h) and recommended filters for the detection of viral contigs in metagenomic samples (∼6 h), and it describes the specific parameters for a nucleotide-sequence-identity-based method of organizing the viral sequences into quasi-species taxonomic-level groups (∼10 min).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.