GenomePhone Frontend

"Ring ring ring ring, GenomePhone"

Introduction

Variant calling is a process in bioinformatics that identifies differences in a genomic sequence compared to a reference sequence. These differences, or variants, can include single nucleotide polymorphisms (SNPs), insertions, deletions, and others. Variant calling plays a crucial role in understanding the genetic basis of diseases, among other applications.

GenomePhone is a framework for distributed variant calling. This repository, genomephone-frontend, serves as the API frontend for the GenomePhone project. It is written in Python using the FastAPI framework.

The genomephone-frontend is responsible for receiving genomic data, dividing it into manageable chunks, and distributing these chunks to different nodes in a Kubernetes cluster for parallel processing. The results are then collected, combined, and made available for further analysis.

Getting Started

To get started with genomephone-frontend, you’ll need to have Python 3.11 installed on your machine. Once Python is installed, you can clone this repository and install the necessary dependencies.

Clone the Repository

git clone https://github.com/GenomePhone/genomephone-frontend.git
cd genomephone-frontend

Install Dependencies

pip install poetry
poetry install

Usage

After installing the dependencies, you can start the FastAPI server.

poetry run uvicorn src.main:app --reload

Contributing

We welcome contributions to genomephone-frontend! If you have a feature request, bug report, or proposal, please open an issue on this GitHub repository.

License

genomephone-frontend is licensed under the MIT License. See the LICENSE file for more details.