Tools used for this comparison are microbeannotator, kofamscan, and Anvi'o. Installation was done via mamba on Ubuntu 20.4 (the env.yml file is supplied above as record of versions of software used.
The snakemake workflow is used to run the main analysis and generation of the files. Not all of the figure generation or comparisons were done using the snakemake workflow; however all scripts used to make figures or generate tables are held in the repository.
All scripts used for figure and in the workflow are found in the workflow/scripts/ folder.
- The individual Rscripts are used to generate the figures.
- The python scripts are used to generate figures.