mutagenic-primer-design

Pooled oligo library generation for primer extension-based deep mutational scanning

Installation

In command line, navigate to the directory where you want to install the project and clone the repo

# In this example we're cloning the repo into
# home directory
cd ~
git clone https://github.com/johnpcooper/mutagenic-primer-design.git

Install virtualenv and create an environment inside the mutagenic-primer-design project directory

cd mutagenic-primer-design
pip install virtualenv
python -m venv .spikedisplay

Activate the environment

source .spikedisplay/bin/activate

Install required packages to the environment

pip install -r requirements.txt

Install spikedisplay package

python setup.py install

Setup jupyter notebook compatability

# Add the .spikedisplay environment to the kernels available in jupyter
python -m ipykernel install --user --name=.spikedisplay

Primer library generation notebook

This notebook contains an example workflow generating a codon-optimized primer library for PCR-based saturating mutagensis the receptor-binding domain of the SARS-CoV-2 spike protein. Library generation can be applied to any open reading frame of interest by changing the input sequence file (in this case located at notebooks/Spike_RBD.txt)

Navigate to the spikedisplay/notebooks directory and open the Primer_Library_Generation.ipynb notebook

# Activate environment
cd ~/mutagenic-primer-design
source .spikedisplay/bin/activate
cd notebooks
jupyter notebook Primer_Library_Generation.ipynb

Run the notebook cell by cell and adjust sequence inputs and other parameters where desired