Tutorial for annotating microbial genomes
Creators
- 1. NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Netherlands
Description
This repository is part of a tutorial that teaches biology students how to:
- download two genomes from NCBI and
- annotate them using several databases such as the COGs, arCOGS, KOs, PFAM, …
- combine the results into one comprehensive table.
The actual tutorial can be found on [Github](https://ndombrowski.github.io/Annotation_workflow/).
The goal of this repository is to provide any custom scripts or databases to run the majority of the tutorial. Specifically, you download the following:
- 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
- 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.
- taxonomy5.txt.gz contains a mapping file that links the ncbi taxonomy ID to a more informative taxonomy string