Software: VADR
Description
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.
Available Versions
| Unspecified: | 1.4.1 1.4.2 1.5.0 |
|---|
Docker hub: https://hub.docker.com/r/staphb/vadr
Home page: https://github.com/ncbi/vadr
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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