Vadr

Introduction

VADR is a suite of tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes or gene families. It has been mainly tested for analysis of Norovirus, Dengue, and SARS-CoV-2 virus sequences in preparation for submission to the GenBank database.

For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/vadr
Home page: https://github.com/ncbi/vadr

Versions

  • 1.4.1

  • 1.4.2

  • 1.5

Commands

  • parse_blast.pl

  • v-annotate.pl

  • v-build.pl

  • v-test.pl

Module

You can load the modules by:

module load biocontainers
module load vadr

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run vadr on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=vadr
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers vadr

v-annotate.pl noro.9.fa va-noro.9