The goal of the tutorial is to provide all the tools to annotate microbial genomes using various databases such as the PFAMs, KOs, etc... For this tutorial we download and analyse 2 genomes from NCBI but it can be easily adjusted to work for your own data. Specifically, you can download with this tutorial: - the tutorial itself as R markdown (.rmd) and HTML format. Notice: The file *trimmed* is a workflow were less database searches were included for a speed-up versions suited for shorter lessons - Databases.tar.gz contains any databases required to run this workflow (the paths from where the data was originally obtained can be found in the tutorial notebook - Databases_for_trimmed_analyses.tar.gz contains any databases required to run the trimmed workflow (the paths from where the data was originally obtained can be found in the tutorial notebook - Custom_Scripts.tar.gz contains any custom scripts needed to run this workflow - Example_data.tar.gz contains examples for the individual output files. This includes the whole analysis as well as a "trimmed" analysis were less database searches were included for a speed-up versions suited for shorter lessons.