Panaroo

Introduction

Panaroo is an updated pipeline for pangenome investigation.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/panaroo
Home page: https://github.com/gtonkinhill/panaroo

Versions

  • 1.2.10

Commands

  • panaroo

  • panaroo-extract-gene

  • panaroo-filter-pa

  • panaroo-fmg

  • panaroo-gene-neighbourhood

  • panaroo-img

  • panaroo-integrate

  • panaroo-merge

  • panaroo-msa

  • panaroo-plot-abundance

  • panaroo-qc

  • panaroo-spydrpick

Module

You can load the modules by:

module load biocontainers
module load panaroo

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 panaroo on our clusters:

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

module --force purge
ml biocontainers panaroo

panaroo -i gff/*.gff -o results --clean-mode strict