An HTML discussing the full workflow can be found under HERE.
This workflow provides a step-by-step tutorial on 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.
This repository provides:
- a detailed, step by step guide on how to annotate microbial genomes (both html and raw md document)
- example files generated during this workflow
- custom scripts that might be needed to run this workflow
Example output files for all steps can be downloaded from here.
All databases and custom scripts are available on ada (for people working at NIOZ). If you follow this tutorial on your own server, all scripts and databases are available on zenodo. If you use this work please cite: Dombrowski, N. et al. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nature Communications 11, 3939 (2020).
If you found this tutorial useful, please cite the following study as we used this study to shape the tutorial:
Dombrowski, Nina, Tom A. Williams, Jiarui Sun, Benjamin J. Woodcroft, Jun-Hoe Lee, Bui Quang Minh, Christian Rinke, and Anja Spang. ‘Undinarchaeota Illuminate DPANN Phylogeny and the Impact of Gene Transfer on Archaeal Evolution’. Nature Communications 11, no. 1 (7 August 2020): 3939. https://doi.org/10.1038/s41467-020-17408-w.