METAVIR pipeline

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

Additional information

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Publications for METAVIR

METAVIR IN pipelines

PMCID: 5253355
PMID: 28167933
DOI: 10.3389/fmicb.2017.00013

[…] only 305 of these proteins were found on contigs that encoded at least one confirmed viral protein, i.e., may potentially represent viral genes. for 51% of these proteins the score from metavir was less than half of the top score. to avoid false viral annotation, we did not include these proteins into our final viral protein dataset. furthermore, we identified eight proteins […]

PMCID: 5253355
PMID: 28167933
DOI: 10.3389/fmicb.2017.00013

[…] had pfam annotations indicating viral origin, and 392 proteins that had matched viral proteins in the refseq-p and/or ncbi-nr databases (max 1.0e-4, min bit-score 45), but had not been detected by metavir. our final dataset of predicted viral proteins therefore consisted of 1674 sequences (table s2)., to determine the lca affiliation for these proteins, we repeated blastp against the viral […]

PMCID: 4728574
PMID: 26761024
DOI: 10.3390/v8010014

[…] version 3 as supplied by illumina were removed using bowtie2 at the default settings (version 2.2.3). of the post-quality control (qc) forward read files, random subsets were taken for submission to metavir [39,40] which has a limit of 2.5 million reads per metavirome., the post-qc reads were assembled using clc genomics workbench as paired files (3 × 2 read files per site), using the default […]

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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