"Ring ring ring ring, GenomePhone"
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.
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.
git clone https://github.com/GenomePhone/genomephone-frontend.git
cd genomephone-frontendAfter installing the dependencies, you can start the FastAPI server.
poetry run uvicorn src.main:app --reloadWe welcome contributions to genomephone-frontend! If you have a feature request, bug report, or proposal, please open an issue on this GitHub repository.