Gubbins¶

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. The gubbins bundle packages version 3.3.

UFS HPC Usage Example¶

The following command can be executed in the terminal to load the bundle:

1	`module load gubbins`

The Gubbins utilities can be run as shown as below:

1 2	`gubbins gubbins_alignment_checker.py`

The gubbins_shell commmand can be used to access a shell in the gubbins bundle.

1	`gubbins_shell`

Performance Notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

UFS HPC Community Guides and Tutorials¶

No community guides available.

Official site and documentation¶

Licensing Information¶

Gubbins is licensed under the GPLv2 license.

Primary citation¶

External Guides and Resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za