query_pan_genome
high speed stand alone pan genome pipeline
Install
- All systems
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curl cmd.cat/query_pan_genome.sh
- Debian
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apt-get install roary - Ubuntu
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apt-get install roary - Kali Linux
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apt-get install roary - Windows (WSL2)
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sudo apt-get updatesudo apt-get install roary - Raspbian
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apt-get install roary - Dockerfile
- dockerfile.run/query_pan_genome
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.