Gubbins

This is the landing page for Gubbins which contains examples, tutorials and other contributed resources for using R on the UFS HPC

UFS HPC usage example

Follow these steps to get started:

First load the gubbins module (currently the version latest version of Gubbins is v3.1.3)
```
$ module load gubbins/3.1.3
```
Next, initialize the Gubbins enviroment by issuing the command:
```
$ gubbins_init
```

You may now use Gubbins as advertised. Here are two examples from the official manual:

$ run_gubbins.py --prefix PMEN1 --first-tree-builder rapidnj --first-model JC --tree-builder raxmlng --model GTR PMEN1.aln

$ run_gubbins.py --prefix ST239 --first-tree-builder rapidnj --first-model JC --tree-builder raxmlng --model GTR ST239.aln

UFS HPC Community Guides and Tutorials

{contributed_guide}

Official site and documentation

Site
Manual

Licensing Information

Gubbins is free software, licensed under GPLv2.

Primary citation

Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R. "Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins". doi:10.1093/nar/gku1196, Nucleic Acids Research, 2014.

Please remember to cite any additional methods used. Check the log file after each run for these additional citations.

External Guides and Resources

No external guides are available.
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

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