metagenomics_pooling_notebook

A Jupyter notebook to assist wet lab shotgun pipeline.

Installation

To install this notebook, first clone the repository from GitHub:

git clone https://github.com/biocore/metagenomics_pooling_notebook.git

Create a Python3 Conda environment in which to run the notebook:

conda create -n pooling_nb 'python>=3.6' scipy numpy matplotlib pandas

Activate the Conda environment:

source activate pooling_nb

Change directory to the downloaded repository folder and install:

cd metagenomics_pooling_notebook
pip install -e '.[all]'

Finally, to enable the notebook Table of Contents, activate the required nbextensions:

jupyter contrib nbextension install --sys-prefix --skip-running-check
jupyter nbextension enable toc2/main

Use

The notebook itself contains detailed usage instructions.

Ideally, you will copy this original notebook and use it for each plate you create with the shotgun pipeline.

Just make sure to activate the right Conda environment before starting the notebook.

Here's a quick example:

cp metagenomics_pooling.ipynb ~/New_project/new_project_pooling.ipynb
cd ~/New_project
source activate pooling_nb
jupyter notebook