Bedford Basin disturbance analysis

We determined the resistance and resilience of the microbial community in the Bedford Basin in response to rainfall events of varying frequency, and intensity.

Structure of the starting repository

root/
├── data/
│   ├── raw/
│   │  └── raw_reads.fastq.gz  
│   └── processed/
│      ├── METADATA.tsv
│      ├── MANIFEST.tsv
│      └── clean_and_processed_reads.qza
│
├── notebooks/
│   ├── 01_metadata_validation.ipynb
│   ├── 02_prelim_data_analysis.ipynb    #alpha, beta, composition analyses
│   └── ...
│
├── scripts/
│   ├── preprocessing.sh
│   └── utils.py                         #python functions for notebooks
│
├── outputs/                             #outputs generated
│
├── README.md
└── environment.yml

Datasets

Dataset	Community	Link
Sequencing
METADATA

Generate the data

Run preprocessing.sh and generate_data.sh from the cloned repo, then open the scripts in order and run all.

Final repository