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Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by e.g. Prokka ) and calculates the pan genome.


Free to use and open source under GNU GPLv3.


  • Roary 3.13.0 is available in Puhti


In Puhti, Roary should be executed as a batch job. An interactive batch job for running Roary can be started with command:

sinteractive -i 

Roaray is installed to Puhti as a part of bioconda environment of Prokka. To use it, you should activate Prokka environment with commands:

export PROJAPPL=/projappl/your_project_name
module load bioconda
source activate prokka
After that you can launch Roary with command roary. For example:
roary -f ./demo -e -n -v ./gff/*.gff

More information

Last update: March 29, 2021