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.
- 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:
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