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.
- Puhti: 3.13.0
In Puhti, Roary should be executed as a batch job. An interactive batch job for running Roary can be started with command:
To use Roary, you should activate Prokka environment with command:
module load prokka
After that you can launch Roary with command
roary. For example:
roary -f ./demo -e -n -v ./gff/*.gff