ArticleBMC bioinformatics2014
Metavir 2: new tools for viral metagenome comparison and assembled virome analysis.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
What it found
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Who cites it
115 citing papers in PubMed.
- Gut Virome: What's the Role in Irritable Bowel Syndrome?Reviews in medical virology · 2025Review
- Gut virome: New key players in the pathogenesis of inflammatory bowel disease.World journal of methodology · 2025Review
- VITALdb: to select the best viroinformatics tools for a desired virus or application.Briefings in bioinformatics · 2025Article
- Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories.Viruses · 2024Review
- Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle.Veterinary research communications · 2024Review
- From Whole Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool.Methods in molecular biology (Clifton, N.J.) · 2024Article
- MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets.ISME communications · 2023Article
- Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data.Microbiome · 2023Article
- Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses.Viruses · 2023Review
- Enhanced Viral Metagenomics with Lazypipe 2.Viruses · 2023Article
- Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach.Viruses · 2023Review
- Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.Microorganisms · 2022Review
- PathoLive-Real-Time Pathogen Identification from Metagenomic Illumina Datasets.Life (Basel, Switzerland) · 2022Article
- The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease.Inflammatory bowel diseases · 2022Review
- Revolutionized virome research using systems microbiology approaches.Experimental biology and medicine (Maywood, N.J.) · 2022Review
- The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes.Microbiology spectrum · 2022Article
- VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data.Microbiology spectrum · 2022Article
- Article
- Using metagenomic data to boost protein structure prediction and discovery.Computational and structural biotechnology journal · 2022Review
- LABRADOR-A Computational Workflow for Virus Detection in High-Throughput Sequencing Data.Viruses · 2021Article
55 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
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities. Following recent advances in sequencing technologies, new challenges arise for existing bioinformatic tools dedicated to viral metagenome (i.e. virome) analysis as (i) the number of viromes is rapidly growing and (ii) large genomic fragments can now be obtained by assembling the huge amount of sequence data generated for each metagenome.
resultsTo face these challenges, a new version of Metavir was developed. First, all Metavir tools have been adapted to support comparative analysis of viromes in order to improve the analysis of multiple datasets. In addition to the sequence comparison previously provided, viromes can now be compared through their k-mer frequencies, their taxonomic compositions, recruitment plots and phylogenetic trees containing sequences from different datasets. Second, a new section has been specifically designed to handle assembled viromes made of thousands of large genomic fragments (i.e. contigs). This section includes an annotation pipeline for uploaded viral contigs (gene prediction, similarity search against reference viral genomes and protein domains) and an extensive comparison between contigs and reference genomes. Contigs and their annotations can be explored on the website through specifically developed dynamic genomic maps and interactive networks.
conclusionsThe new features of Metavir 2 allow users to explore and analyze viromes composed of raw reads or assembled fragments through a set of adapted tools and a user-friendly interface.
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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.