Roary

Overview

Roary is a pan genome pipeline which can take GFF3 data output by Prokka and calculate the pan genome

Availability

Cluster	Module/Version
BOSE	roary/3.13.0
BGSC	Not Available

Note: You can simply use module load roary to activate the most recently installed version of this software.

Arguments / Options

This is a list of arguments for the roary command that we wanted to highlight. Use roary --help for a full list.

Option	Description
-p	Number of threads
-o	Output file name
-h	Help

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load roary    # Load Roary
roary

Real Example

Has your research group used Roary in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of Roary. Further details are available at the top of the help page when you use the command roary --help.

"Roary: Rapid large-scale prokaryote pan genome analysis", 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). doi: http://dx.doi.org/10.1093/bioinformatics/btv421