METAVIR protocols

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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 No

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Publications for METAVIR

METAVIR in pipelines

PMCID: 5474096
PMID: 28630803
DOI: 10.7717/peerj.3428

[…] pipeline. the assembled contigs were then confirmed to be viral in origin using the virsorter software with default settings (; ). the viral fraction of the etnp metagenomic dataset was uploaded to metavir 2 () and those contigs larger than 1,000 bp and with three or more orfs, at least one of which affiliated to a reference archaeal virus or archaeal virus pathway, were considered […]

PMCID: 5635123
PMID: 29018269
DOI: 10.1038/s41598-017-12885-4

[…] clinical and epidemiological characteristics (see statistical analysis section).abbreviations: or, odds ratio; aor, adjusted odds ratio; 95%ci, 95% confidence interval; f ≥ 3, advanced fibrosis(metavir); a3, severe activity grade (metavir); apri, aspartate aminotransferase to platelet ratio index; fpr, fibrosis progression rate; adar1, double-stranded rna-specific adenosine deaminase; hcv, […]

PMCID: 4771703
PMID: 26927795
DOI: 10.1371/journal.pone.0150361

[…] family, this 34,467 bp circular contig contains 52 orfs. it is likely that this contig represents a genome of a phage with either circular permutations or long direct terminal repeats. according to metavir blastp and independent blastx analyses, the closest homologs of the lnw4-c12 terl gene are sequences of the terminase large subunit from roseobacter phage rdjl phi 1 (62,668 bp) […]

PMCID: 4360716
PMID: 25852662
DOI: 10.3389/fmicb.2015.00199

[…] a gene prediction with metagene annotator (noguchi et al., ), blastp comparison to ncbi refseq genomes, and hmmer comparison with pfam profiles (punta et al., ), and are publicly available on metavir ( under project “fart4 / far-t4 lake pavin”., using proteins predicted from the far-t4 contigs identified, phylogenies were inferred for different t4 […]

PMCID: 4650499
PMID: 26577924
DOI: 10.1186/s40168-015-0131-4

[…] were carried out using pair-ended reads and sequences less than 50 nt in length were discarded., the composition of the extracted metaviromes was determined using raw paired-end reads using the metavir web server (; []). since metavir has limitations analyzing metaviromes containing more than 2,500,000 sequences, the non-assembled datasets (metavirome) […]

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METAVIR in publications

PMCID: 5919507
PMID: 29698472
DOI: 10.1371/journal.pone.0196486

[…] an use assessment was classified as reliable with a success rate of ≥ 60%., use reference values for arfi quantification and 2d-swe with histological scoring system for fibrosis staging according to metavir: f0-1 = no or minimal fibrosis, f2 = significant fibrosis, f3 = severe fibrosis, f4 = cirrhosis [,,]. 2d-swe reference values were transformed from stiffness (kpa) to sws (m/s)., statistical […]

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

[…] filtering and taxonomic clustering—i.e., grouping reads according to their respective taxa before assembly. assembly improvement by taxonomic clustering is exemplified in five workflows: metavir (roux et al., ), rins (bhaduri et al., ), virusfinder (wang et al., ), surpi (in comprehensive mode) (naccache et al., ), and vip (li et al., ). two of the discussed workflows have multiple […]

PMCID: 5940400
PMID: 29765541
DOI: 10.18632/oncotarget.25092

[…] inc, tokyo, japan) using standardized enzymatic procedures and evaluated tg (mg/dl), tc (mg/dl), hdlc (mg/dl) and ldlc (mg/dl). fibrosis stage has performed by liver biopsy and evaluated by metavir score., sustained virological response (svr) was defined as negative hcv rna at 6-month after cessation of treatment. the four indexes for fibrosis (fib4) was calculated following formula […]

PMCID: 5946635
PMID: 29770228
DOI: 10.1177/2058460118768363

[…] our swvs results with cut-off values (m/s) for predicting the stages of fibrosis described by lupsor et al. () (f ≥ 1: 1.19; f ≥ 2: 1.34; f ≥ 3: 1.61; and f ≥ 4: 2.00) and sporea et al. () based on metavir staging system (f ≥ 1: 1.19; f ≥ 2: 1.21; f ≥ 3: 1.58; and f ≥ 4: 1.82) in the assumption that healthy participants belong to the f0 stage (no known history of liver disease with normal liver […]

PMCID: 5907308
DOI: 10.1186/s13098-018-0315-8

[…] analysis. posteriorly, each patient had their liver fibrosis levels esteemed through three scores: • bard: results ≥ 2 = f3–f4, with negative predictive values of 97%. • nafld: results < − 1455 = metavir f0 (no fibrosis), f1 (minimal fibrosis) or f2 (moderate fibrosis); values > 0675 = metavir f3 (advanced fibrosis) and f4 (liver fibrosis); intermediary levels = undetermined fibrosis. • […]

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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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