Software: Gubbins
Description
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.
Available Versions
| Unspecified: | 3.2.0 3.3.0 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/gubbins and its home page on Github.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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