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Protocols

VirSorter specifications

Information


Unique identifier OMICS_11702
Name VirSorter
Interface Web user interface
Restrictions to use None
Input data Microbial genome(s) (draft or completely assembled)
Input format FASTA
Output data FASTA, GenBank, CSV
Computer skills Basic
Version 1.0.2
Stability Stable
Maintained Yes

Maintainer


  • person_outline Simon Roux

Information


Unique identifier OMICS_11702
Name VirSorter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Microbial genome(s) (draft or completely assembled)
Input format FASTA
Output data FASTA, GenBank, CSV
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
HMMER, MCL, Metagene Annotator, MUSCLE, BLAST
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Simon Roux

Publication for VirSorter

VirSorter citations

 (33)
library_books

Overview of Virus Metagenomic Classification Methods and Their Biological Applications

2018
Front Microbiol
PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] earch program is HMMER (Mistry et al., ). ClassyFlu (Van der Auwera et al., ) and vFam (Skewes-Cox et al., ) rely exclusively on HMM searches, while VMGAP (Lorenzi et al., ), Metavir (Roux et al., ), VirSorter (Roux et al., ), and MetLab can also use HMMER.All of these search methods are examples of similarity search—homology or alignment-based methods. The other search method is composition searc […]

library_books

Reproducible protocols for metagenomic analysis of human faecal phageomes

2018
Microbiome
PMCID: 5892011
PMID: 29631623
DOI: 10.1186/s40168-018-0446-z

[…] eference set when contigs aligned to each other with at least 90% identity over 90% of their length. In order for a contig to be included in the final analysis, it must have been detected as viral by Virsorter [] in the phageome decontamation mode, or had a significant BLAST hit (50% identity over 90% of the length) to a genome in RefSeq Virus [, ], or had no significant BLAST hits (alignments lon […]

call_split

Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code

2018
Virus Evol
PMCID: 5888411
PMID: 29644096
DOI: 10.1093/ve/vey008
call_split See protocol

[…] For identification of bacteriophages, scaffolds >1 kb were classified using VirSorter (decontamination mode; ). Only scaffolds assigned to Categories 1 and 2 were considered bacteriophage contigs and were filtered for redundancy at 95% nt identity over 70% of the length using […]

library_books

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

2018
Environ Microbiol
PMCID: 5900883
PMID: 29327410
DOI: 10.1111/1462-2920.14043

[…] The genomes were screened for the presence of prophages using VirSorter (Roux et al., ) and PHASTER (Arndt et al., ). Prophage predictions were manually curated to remove false‐positives and verify prophage ends, leading to a total of 35 prophages identified. Pr […]

library_books

Extension of the viral ecology in humans using viral profile hidden Markov models

2018
PLoS One
PMCID: 5774701
PMID: 29351302
DOI: 10.1371/journal.pone.0190938

[…] ment of viral sequence classification and abundance estimations methods is essential.There are also other tools and protocols available for detecting viral genomes in microbial genomic data. The tool Virsorter[] uses a reference set consisting of viral proteins from the RefSeq database (similar to pVOGS[]) but this tool and its database are mainly designed to detect viruses that infect microbes (a […]

library_books

Multi omics Reveals the Lifestyle of the Acidophilic, Mineral Oxidizing Model Species Leptospirillum ferriphilumT

2018
Appl Environ Microbiol
PMCID: 5772234
PMID: 29150517
DOI: 10.1128/AEM.02091-17

[…] l material). Contig 1 was 2,569,357 bases with a depth of coverage of 574-fold, while contig 2 was 41,141 bases with a depth of coverage of 33-fold. Contig 2 was predicted to be a putative phage with VIRSorter (), and a region on contig 1 with high similarity to contig 2 putatively represents a prophage. Although further analysis is required to determine its origin, contig 2 was excluded due to it […]

Citations

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VirSorter institution(s)
Ecology and Evolutionary Biology, University of Arizona, AZ, USA; Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes: Génome et Environnement”, Clermont-Ferrand, France; CNRS UMR 6023, LMGE, Aubière, France; Department of Agricultural and Biosystems Engineering, University of Arizona, AZ, USA
VirSorter funding source(s)
Gordon and Betty Moore Foundation #3790; University of Arizona Ecosystem Genomics Institute

VirSorter review

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Anonymous user #54894

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Web
VirSorter is a tool can be easily used. It has augmented viruses databases with sampled genomes. It allows user to add viral genome sequences to the database according to their paper. It also performs comparable to other tools in terms of complete genome, and outperforms in single-cell amplified genome sequencing data.
As it uses hmmsearch in searching protein profile database, it can provide predictions of novel phages beyond 'known' database, which I find quite interesting.
It has different confidence categories, which I find very useful.