PrimerDriver: Automated design of mutagenic PCR primers

Introduction

PrimerDriver is a user-friendly bioinformatics platform specifically designed to generate primers for site-directed mutagenesis experiments into workflows with an easy-to-use command-line interface. “Traversing” PrimerDriver lanes, users can generate possible mutagenic primers upon input of a DNA sequence (DNA), design primers for an array of species codon expression systems through direct mutation of the amino acid (PRO), characterize and report user-designed primers (CHAR).

Usage

A. Running standalone

You can access and download the CLI from the releases page. Currently, we only have prebuilt binaries for 64-bit Windows and Linux. For other OS/architectures, see the section on Building from Source, under Developing Locally.

Run the program in a terminal using

primerdriver -h

This will run the help program. For first-time users, the program can be run in interactive mode by passing the -i flag:

primerdriver -i

This will walk you through each option step-by-step. Batch design can be performed by including primerdriver as part of a shell script.

B. Running as Python module

Prerequisites

• Git
• Mise

Setup

1. Clone the repo to your local device and cd into it

   git clone https://github.com/kvdomingo/primerdriver.git
   cd primerdriver
   

2. Install dependencies:

   mise install
   

Run the program as follows:

poetry run python -m primerdriver -h

C. Running from Docker

Run as follows:

docker run -it --entrypoint python kvdomingo/primerdriver -m primerdriver -h

Web application

For a more interactive experience, visit the web application.

Documentation

The documentation is available at https://primerdriver-docs.kvd.studio.

Contributing

Open a PR or raise an issue. You may also email Nomer or Kenneth, depending on the nature of the issue.

Developing locally

Prerequisites

• Docker
• Mise

Installing

A step by step series of examples that tell you how to get a development environment running

1. Clone the repo.
2. Install prerequisites:

   mise install
   pip install -U pre-commit
   pre-commit install
   

3. Install backend dependencies:

   poetry install --no-root --with dev
   

4. Run the development servers:

   task
   

Wait a few minutes for all the containers to start, then access the local servers in your browser at:

• Web app: http://localhost:3000
• Docs: http://localhost:8000

Building from source

Run the script:

# On a Linux machine, will build for Linux x64 only
# On a Windows machine, will build for Windows and Linux x64
task build

Deployment

git add .
git commit -m "DESCRIPTIVE_COMMIT_MESSAGE"
git push origin your_feature_branch

where your_feature_branch should summarize the changes you are implementing following the Conventional Commits format (e.g., feat/xxxx, fix/yyyy).

Authors

• Numeriano Amer "Nomer" E. Gutierrez - Project Lead, Molecular Biologist - Email | GitHub
• Kenneth V. Domingo - Technical Lead - Email | Website | GitHub
• Shebna Rose D. Fabilloren - Technical Consultant - Email
• Carlo M. Lapid - Project Adviser - Email

Versioning

This project complies with SemVer for versioning. For all available versions, see tags.

License

This project is licensed under the GPLv3 License.