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.
Simply open the Notebook link here.
Alternatively view the Notebook by pasting the address into nbviewer.
Click the icons below to launch one of the two options:
- via Google colab
- via Binder
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:
- Installation via pip
pip3 install jupyter biopython
For installation without root access add the --user flag.
- Installation via conda
conda env create -f environment.yml
conda activate biopython-coronavirus
Open the Notebook as follows:
jupyter-notebook biopython-coronavirus-notebook.ipynb