Roary¶

Roary is a high speed stand alone pan genome pipeline. The bundle packages version 3.13.0.

Usage example¶

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

1	`module load roary`

The module makes the following commands available:

iterative_cdhit
roary
roary-pan_genome_reorder_spreadsheet
roary-query_pan_genome
roary-unique_genes_per_sample

The roary_shell command can be used to access a shell in the bundle.

Run pet list -t roary for a list of examples.

Performance notes¶

No performance notes available

Recommended resources¶

Roary should be run on a system with at least 16 GB of RAM and 8 threads.

Benchmarks¶

No benchmarks available.

Community guides and tutorials¶

No community guides available.

Official site and documentation¶

Licensing information¶

Roary is licensed under the GPLv3 license.

Primary citation¶

Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, Bioinformatics, (2015). "Roary: Rapid large-scale prokaryote pan genome analysis". doi

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