biopython-coronavirus

A tutorial Jupyter Notebook illustrating how to use Biopython to identity and perform some basic characterization of a coronavirus genome sequence. The objective of this tutorial is to introduce some of the Biopython modules in an applied biological context. Note, the use of a coronavirus genome is merely illustrative, the analyses are generic, and could be applied to any small genome.

Viewing the Notebook

Simply open the Notebook link here.

Alternatively view the Notebook by pasting the address into nbviewer.

Running the Notebook online

Click the icons below to launch one of the two options:

1. via Google colab

2. via Binder

Running the Notebook locally

First clone this repository:

git clone https://github.com/chris-rands/biopython-coronavirus;
cd biopython-coronavirus

Requires Python (version 3.6 or higher) with the jupyter and biopython modules. One of two options is recommended:

1. Installation via pip

pip3 install jupyter biopython

For installation without root access add the --user flag.

2. Installation via conda

conda env create -f environment.yml
conda activate biopython-coronavirus

Open the Notebook as follows:

jupyter-notebook biopython-coronavirus-notebook.ipynb

Related Biopython resources

• Official tutorial documentation
• Peter's workshop
• Notebook tutorials