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GubbinsΒΆ

Genealogies Unbiased By recomBinations In Nucleotide Sequences - Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.

Gubbins is made available on the cluster as a shared Apptainer container image.

You can use the apptainer/gubbins module which will add convenient aliases to Gubbins scripts, such as run_gubbins.py, which will run within the container.

To use any of the aliases in a non-interactive/SLURM batch script, add the following in your script before using the alias: shopt -s expand_aliases.

See the Gubbins manual for usage information. Example:

Terminal

module load apptainer/gubbins
# The following is required to use aliases in a non-interactive/SLURM batch script:
shopt -s expand_aliases
run_gubbins.py <FASTA alignment>