The scikit-bio cookbook: delicious and nutritious bioinformatics recipes

This series of Jupyter Notebooks contains executable "recipes" for bioinformatics workflows using scikit-bio.

Readers interested in gaining more background information on bioinformatics may want to start with An Introduction to Applied Bioinformatics, which makes extensive use of scikit-bio to teach concepts in bioinformatics.

This is not the main scikit-bio documentation. You can find the latest scikit-bio API documentation here.

These notebooks are only tested to work with scikit-bio 0.5.0, which requires Python 3.4 or later. The notebooks may not work with other versions of scikit-bio. Click here to view scikit-bio 0.5.0 API documentation.

Reading the scikit-bio cookbook

There are two ways to read the scikit-bio cookbook.

The easiest way is to read the static online version.

The recommended way is to install the interactive version and read it locally. This will let you exectute and experiment with the recipes from within your web browser. To view and interact with the notebooks, you'll need Python 3.4 or later, scikit-bio 0.5.0, and the Jupyter Notebook installed.

The easiest and recommended way to install these dependencies is via the conda package manager available in Anaconda or miniconda. Once you have conda installed, create a new environment with the following packages:

conda create -c -n scikit-bio-cookbook python=3.5 scikit-bio=0.5.0 jupyter requests

Activate the environment:

source activate scikit-bio-cookbook

Install extra (non-conda) dependencies needed for recipes:

pip install ete3 qiime-default-reference

Next, you'll need to download the scikit-bio cookbook. We recommend pulling the latest version from GitHub (you may need to install git first), and then changing to the new directory that is created:

git clone
cd scikit-bio-cookbook

Finally, start the Jupyter Notebook server:

jupyter notebook Index.ipynb

<img title="Powered by scikit-bio" src="" align=center height=50/>