create_pan_genome

high speed stand alone pan genome pipeline

Install

All systems
curl cmd.cat/create_pan_genome.sh
Debian Debian
apt-get install roary
Ubuntu
apt-get install roary
image/svg+xml Kali Linux
apt-get install roary
Raspbian
apt-get install roary

roary

high speed stand alone pan genome pipeline

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes.