1 Analysis
All genomes were reannotated with prokka using the script 03-prokka.snakefile, and subdivided into groups by species, as determined by ANIm analysis, in the subdirectory assets/analysis/2021-08-19_split_genomes, using the script split_species.py.
These genomes were then analysed by roary v3.12.0 using the script 04-roary.sh.
2 Output
roary output is subdivided by species group in the subdirectory assets/analysis/2021-08-19_roary.