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Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

Simon Roux12, Jeremy Tournayre12, Antoine Mahul3, Didier Debroas12 and François Enault12*

Author Affiliations

1 Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France

2 CNRS, UMR 6023, LMGE, Aubiere, France

3 Centre Régional de Ressources Informatiques, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France

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BMC Bioinformatics 2014, 15:76  doi:10.1186/1471-2105-15-76

Published: 19 March 2014

Abstract

Background

Metagenomics, 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.

Results

To 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.

Conclusions

The 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.

Keywords:
Virus; Phage; Metagenomics; Web server