ArticleBMC genomics2016
ViromeScan: a new tool for metagenomic viral community profiling.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- Metagenomic profiling reveals distinct signatures of pathogens, antibiotic-resistance genes and human viruses in urban river mouths of the north-western Adriatic coast.Scientific reports · 2026Article
- Gut Virome: What's the Role in Irritable Bowel Syndrome?Reviews in medical virology · 2025Review
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- HPV-KITE: sequence analysis software for rapid HPV genotype detection.Briefings in bioinformatics · 2025Article
- VITALdb: to select the best viroinformatics tools for a desired virus or application.Briefings in bioinformatics · 2025Article
- Microbial landscape of Indian homes: the microbial diversity, pathogens and antimicrobial resistome in urban residential spaces.Environmental microbiome · 2025Article
- Exploration of fecal microbiota in newly diagnosed patients with inflammatory bowel disease using shotgun metagenomics.Frontiers in cellular and infection microbiology · 2025Article
- VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.Molecular biology and evolution · 2024Article
- Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence.Neural regeneration research · 2024Review
- Benchmarking informatics approaches for virus discovery: caution is needed when combiningmSystems · 2024Article
- From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species.Methods in molecular biology (Clifton, N.J.) · 2024Article
- CAPTVRED: an automated pipeline for viral tracking and discovery from capture-based metagenomics samples.Bioinformatics advances · 2024Article
- From Whole Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community.Journal of virology · 2023Article
- Current trends in RNA virus detection through metatranscriptome sequencing data.FEBS open bio · 2023Review
- Agnostic Sequencing for Detection of Viral Pathogens.Clinical microbiology reviews · 2023Review
- DETIRE: a hybrid deep learning model for identifying viral sequences from metagenomes.Frontiers in microbiology · 2023Article
- Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Development and Validation of a Bioinformatic Workflow for the Rapid Detection of Viruses in Biosecurity.Viruses · 2022Article
- LABRADOR-A Computational Workflow for Virus Detection in High-Throughput Sequencing Data.Viruses · 2021Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBioinformatics tools available for metagenomic sequencing analysis are principally devoted to the identification of microorganisms populating an ecological niche, but they usually do not consider viruses. Only some software have been designed to profile the viral sequences, however they are not efficient in the characterization of viruses in the context of complex communities, like the intestinal microbiota, containing bacteria, archeabacteria, eukaryotic microorganisms and viruses. In any case, a comprehensive description of the host-microbiota interactions can not ignore the profile of eukaryotic viruses within the virome, as viruses are definitely critical for the regulation of the host immunophenotype.
resultsViromeScan is an innovative metagenomic analysis tool that characterizes the taxonomy of the virome directly from raw data of next-generation sequencing. The tool uses hierarchical databases for eukaryotic viruses to unambiguously assign reads to viral species more accurately and >1000 fold faster than other existing approaches. We validated ViromeScan on synthetic microbial communities and applied it on metagenomic samples of the Human Microbiome Project, providing a sensitive eukaryotic virome profiling of different human body sites.
conclusionsViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples from reads of other microorganisms. This implies that users can fully characterize the microbiome, including bacteria and viruses, by shotgun metagenomic sequencing followed by different bioinformatic pipelines.
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