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METAVIR specifications


Unique identifier OMICS_03513
Interface Web user interface
Restrictions to use None
Input data Some sequence datasets composed of short reads or assembled contigs.
Output format FASTA
Biological technology Illumina
Programming languages Javascript, Perl, PHP, R
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

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Publications for METAVIR

METAVIR citations


Overview of Virus Metagenomic Classification Methods and Their Biological Applications

Front Microbiol
PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] D, Clinical PathoScope, DUDes, EnsembleAssembler, FACS, Kraken, LMAT, Metavir, MetLab, SMART, Taxonomer and Virana), or hours (19 workflows: Giant Virus Finder, GOTTCHA, IMSA, MEGAN, MePIC, MetaShot, Metavir 2, NBC, ProViDE, Readscan, Rega Typing Tool, RIEMS, RINS, SLIM, SURPI, Taxy-Pro, “Unknown pathogens from mixed clinical samples,” VIP and ViromeScan), or even days (5 workflows: Exhaustive Ite […]


Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater

PLoS One
PMCID: 5882159
PMID: 29614100
DOI: 10.1371/journal.pone.0195350

[…] ST (the Metagenomics RAST) server version 3.5 []. Aw et al. [] (referred to as ‘Aw’) virtigs were retrieved from MG-RAST for re-analysis. Wastewater virtigs from this study and Aw were compared using MetaVir 2 tools (available at [] and also MG-RAST analysis. Analysis of the virtigs can be re-created at the MetaVir 2 server (i.e., “wastewater phage”). Open reading f […]


Deciphering the Human Virome with Single Virus Genomics and Metagenomics

PMCID: 5869506
PMID: 29509721
DOI: 10.3390/v10030113

[…] m a previous salivary survey [] (maximum length = 349 pb) were reassembled using SPAdes assembler version 3.6.1, with --iontorrent and only-assembler options. General automated annotation was done in metavir [] and JGI-IMG []. Accurate annotation of vSAG 92-C3 was achieved by comparing predicted proteins with the nr database (National Center for Biotechnology Information (NCBI)) using BLAST (Basic […]


Exploring Viral Diversity in a Unique South African Soil Habitat

Sci Rep
PMCID: 5758573
PMID: 29311639
DOI: 10.1038/s41598-017-18461-0
call_split See protocol

[…] an N50 of 2,047 and a maximum of 47,854 bases.The processed reads were assembled de novo using CLC Genomics Workbench version 6.0.1 using the default settings. Reads and contigs were uploaded to the MetaVir (, VIROME ( and MG-RAST ( servers for virus diversity estimations. The viromes were uploaded in 2 […]


Metavirome Sequencing of the Termite Gut Reveals the Presence of an Unexplored Bacteriophage Community

Front Microbiol
PMCID: 5759034
PMID: 29354098
DOI: 10.3389/fmicb.2017.02548
call_split See protocol

[…] sembler (Version 3.0) available on the Illumina BaseSpace platform with the default parameters using error correction and assembly mode (Bankevich et al., ). The contigs obtained were uploaded on the Metavir server for taxonomic assignments of the predicted ORFs using RefSeq complete viral genome protein sequence database from NCBI (released on 01/11/2017) (Roux et al., ). All the predicted protei […]


Characterization of ecologically diverse viruses infecting co occurring strains of cosmopolitan hyperhalophilic Bacteroidetes

PMCID: 5776456
PMID: 29099492
DOI: 10.1038/ismej.2017.175

[…] arge contigs (over 20 kb) that were then merged as described in . Functional annotation of predicted genes from virus metagenomes were carried out using JGI (IMG/M ER: and MetaVir (). […]


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METAVIR institution(s)
Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France; CNRS, UMR 6023, LMGE, Aubiere, France; Centre Régional de Ressources Informatiques, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
METAVIR funding source(s)
Supported by a PhD grant from the French defense procurement agency (DGA, Direction Générale de l’Armement).

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