Software: Pandora
Description
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.
Available Versions
| Unspecified: | 0.9.1 |
|---|
BioContainers: https://biocontainers.pro/tools/pandora
Home page: https://github.com/rmcolq/pandora
Commands
- pandora
Module
You can load the modules by:
module load biocontainers
module load pandora
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 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