Pandora

Introduction

Pandora is a tool for bacterial genome analysis using a pangenome reference graph (PanRG). It allows gene presence/absence detection and genotyping of SNPs, indels and longer variants in one or a number of samples.

For more information, please check:

Versions

  • 0.9.1

Commands

  • pandora

Module

You can load the modules by:

module load biocontainers
module load pandora

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 pandora on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=pandora
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers pandora

pandora index -t 4 GC00006032.fa