Repository for the AWI-Gen 2 microbiome project workflows, analysis, and results.
Please note that this repository aims to document our analysis approach and is not intended for a full reproduction of the results, since the metadata tables are needed to fully run many of the scripts. Given the nature of the project, the metadata tables are available from EGA only after approval from the relevant data access committee.
Please refer to this publication:
Maghini, Ovoduran et al. Expanding the Gut Microbiome Atlas of Africa Nature 2025
./data/Folder to hold classification and metadata tables../files/Folder to hold derived data tables after running the scripts../figures/Folder to hold figures after running the scripts../src/R code for the analysis./cluster_scripts/Other analysis and data-wrangling scripts that were run on our cluster./workflows/Legacy folder for the nextflow processing workflows
If you have any questions or comments, please feel free to open an issue or contact the corresponding author on the above-mentioned publication.