README

This repository contains the scripts (in jupyter notebooks) to generate the figure in the manuscript "Pangenome mining of the Streptomyces genus redefines their biosynthetic potential".

USAGE

1. Clone this repository

git clone https://github.com/NBChub/Streptomyces_pangenome_ms.git 

2. Set up BGCFlow

# create and activate new conda environment
conda create -n bgcflow pip -y
conda activate bgcflow

# install BGCFlow wrapper
pip install git+https://github.com/NBChub/bgcflow_wrapper.git

# clone BGCFlow to "bgcflow" folder
bgcflow clone bgcflow

2. Set configurations

# edit the location of the bgcflow dir to the right directory with dataset
nano config.yaml

3. Setting up Conda Environments

Install these conda environments:

mamba env create -f python_notebook.yaml
mamba env create -f r_notebook.yaml

4. Run the notebooks

• There are two kind of notebooks, R (.R.ipynb) and python (.python.ipynb)
• Run the notebook using the corresponding conda environment: python_notebook or r_notebook
• Start jupyter session

# for python
conda activate python_notebook
jupyter lab

# for R
conda activate r_notebook
jupyter lab

• Run the notebooks in order

Citation

Mohite et al. (2024). Pangenome mining of the Streptomyces genus redefines their biosynthetic potential. bioRxiv 2023.06.14.545018; doi: https://doi.org/10.1101/2024.02.20.581055