Gubbins

Introduction

Gubbins is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.

For more information, please check its website: https://biocontainers.pro/tools/gubbins and its home page on Github.

Versions

  • 3.2.0

  • 3.3

Commands

  • extract_gubbins_clade.py

  • generate_ska_alignment.py

  • gubbins_alignment_checker.py

  • mask_gubbins_aln.py

  • run_gubbins.py

  • sumlabels.py

  • sumtrees.py

Module

You can load the modules by:

module load biocontainers
module load gubbins

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 Gubbins on our clusters:

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

module --force purge
ml biocontainers gubbins

run_gubbins.py --prefix ST239 ST239.aln