This repository hosts the software used to analyze and generate data for the cll_mouse_microbiome manuscript. The repo consists of 4 directories that are described below:
- src — The code used to analyze shotgun sequence data. The majority of the code is contained within a Jupyter notebook (cll-mouse-microbiome.ipynb), with some helper functions in the file called metagenome_R_functions.R
- data - Data used as input for the analysis code. The shotgun data analyzed here was preprocessed with the metaGnosis pipeline using the config files in the snakemake_config directory. Metaphlan taxa abundance and Humann pathway abundance files are found in the files called merged_abundance_table.tsv and merged_pathabundance_unstratified_cpm.tsv, respectively. Sample metadata is in cll_mouse_microbiome_metadata.tsv.
- env — The Conda environment that was used to run the code in src. Contains a .yaml file that can be used to recreate the environment. The yaml contains comments for other libraries that were installed outside of Conda.
- results — The analysis files outputted by the code can be found in this directory.