VirSorter pipeline

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 citation

2017
PMCID: 5707555

[…] viruses in the hot spring sample., from the 9220 assembled contigs, 84 were predicted by virsorter as being viral in origin, inclusive of all probabilistic categories (i, ii and iii) according to virsorter. only contigs of ≥5 kb in length were retained after this selection, which left 15 viral putative partial/full virus genomes in the nucleotide size range of 5387–26950 nt and read coverages […]

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.