VirSorter protocols

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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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Maintainer


  • person_outline Simon Roux <>

Publication for VirSorter

VirSorter in pipelines

 (4)
2017
PMCID: 5474096
PMID: 28630803
DOI: 10.7717/peerj.3428

[…] of 95 bp was imposed on the entire read dataset. reads were assembled using the soapdenovo software in the mocat 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, […]

2017
PMCID: 5636890
PMID: 29021524
DOI: 10.1038/s41467-017-01086-2

[…] acid identity (aai) percentages were calculated using the enveomics package. for comparison, a similar gene affiliation was applied to contigs from the same lake metagenomes detected as phages by virsorter excluding virophages, and contigs identified as ncldv based on the presence of a ncldv major capsid protein (see below)., whole-genome/contig comparison plots were generated using easyfig. […]

2017
PMCID: 5663388
PMID: 29073070
DOI: 10.1073/pnas.1714821114

[…] in ., to accommodate the large size of the metagenomic datasets, a step-wise assembly and reassembly workflow was implemented to recover viral sequences (). this workflow implemented the tool virsorter () to extract viral sequences from metagenomic assemblies of both size fractions. ultimately, 483 viral scaffolds were recovered and given numerical identifiers with the prefix “vs.” […]

2017
PMCID: 5704599
PMID: 29179741
DOI: 10.1186/s40168-017-0374-3

[…] and columns were clustered by k-means clustering., inputs for viral pcs were the same contigs used to identify viral populations—those contigs greater than 1 kbp and identified by virfinder [] or virsorter [] as being of viral origin. orfs predicted from these viral contigs and microbial orfs were self-clustered (cd-hit -c 0.6 -as 0.8 -g 1 -n 4 -d 0 -m 30000; 60% percent identity and 80% […]


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VirSorter in publications

 (29)
PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] 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 […]

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

[…] steps, in order to select viral contigs and remove as much bacterial dna contamination as possible, contigs were picked which fulfil at least one of the following criteria: (a) predicted as viral by virsorter package []; (b) having sufficient similarity (50% identity over 90% of contig length) to known sequences in the viral section of ncbi refseq database [, ]; (c) being circular; and (d) […]

PMCID: 5888411
PMID: 29644096
DOI: 10.1093/ve/vey008

[…] bats highlight the possibility of consumption of insect-contaminated fruits. however, the real hosts of these viruses are yet to be determined., there were 498 contigs annotated as phages by virsorter. further comparison to genbank showed that they belonged to the myoviridae (74 contigs), podoviridae (22 contigs), and siphoviridae (20 contigs) families, whereas the rest were unassigned […]

PMCID: 5900883
PMID: 29327410
DOI: 10.1111/1462-2920.14043

[…] across the acidobacterial genomes encoding for group 1h/5 [nife]‐hydrogenases can be found in supporting information table s9., 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. […]

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

[…] 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 […]


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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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Qian Yu

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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.