ArticlePeerJ2018
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Infectome Landscape of Rodents and Shrews in Guangdong Province Reveals Diverse Pathogens with Zoonotic Potential in Wildlife.Viruses · 2026Article
- Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes.Nature biotechnology · 2026Article
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- Seasonal enhancement of the viral shunt catalyzes a subsurface oxygen maximum in the Sargasso Sea.Nature communications · 2025Article
- Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome.Environmental microbiome · 2025Article
- Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.Nucleic acids research · 2025Article
- Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression.bioRxiv : the preprint server for biology · 2025Article
- Probe-based metagenomic pathogen detection: advancing laboratory capacity for complex diagnosis.Frontiers in microbiology · 2025Article
- Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.PeerJ · 2025Article
- Virome analyses of Amblyomma cajennense and Rhipicephalus microplus ticks collected in Colombia.Acta tropica · 2024Article
- Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security.Microorganisms · 2024Review
- Hecatomb: an integrated software platform for viral metagenomics.GigaScience · 2024Article
- Identification and classification of the genomes of novel microviruses in poultry slaughterhouse.Frontiers in microbiology · 2024Article
- SnakeLines: integrated set of computational pipelines for sequencing reads.Journal of integrative bioinformatics · 2023Article
- Giant Virus Infection Signatures Are Modulated by Euphotic Zone Depth Strata and Iron Regimes of the Subantarctic Southern Ocean.mSystems · 2023Article
- Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach.Viruses · 2023Review
- Breeding honey bees (Frontiers in insect science · 2023Article
- Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A Metagenomic Investigation of Spatial and Temporal Changes in Sewage Microbiomes across a University Campus.mSystems · 2022Article
- Development and Validation of a Bioinformatic Workflow for the Rapid Detection of Viruses in Biosecurity.Viruses · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.
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Registered trials
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.