Overview

TL;DR / Simpler Version

DNA is like a long code made of A, T, G, and C. Small changes (mutations) in specific parts of this code, like in genes responsible for preventing cancer, can increase a person's risk of developing the disease. For instance, if an 'A' appears where a 'T' should be at a particular spot, that's a mutation. These changes can vary in how harmful they are, and we'll build a tool to analyze these different variations' harmfulness.

Features:

• Evo2 model for variant effect prediction
• Predict pathogenicity of single nucleotide variants (pathogenic/benign)
• Comparison view for existing ClinVar classification vs. Evo2 prediction
• Prediction confidence estimation
• Genome assembly selector (e.g., hg38)
• Select genes from chromosome browsing or searching (e.g., BRCA1)
• See full reference genome sequence (UCSC API)
• Explore gene and variants data (NCBI ClinVar/E-utilities)
• Python backend deployed with Modal
• FastAPI endpoint for variant analysis requests
• GPU-accelerated (H100) variant scoring via Modal
• Responsive Next.js web interface
• Modern UI with Tailwind CSS & Shadcn UI

Evo2 Model

Check out the paper behind the model.

• Paper
• GitHub Repository

Setup

Follow these steps to install and set up the project.

Clone the Repository

git clone --recurse-submodules https://github.com/Andreaswt/variant-analysis-evo2.git

Install Python

Download and install Python if not already installed. Use the link below for guidance on installation: Python Download

Create a virtual environment for each folder, except elevenlabs-clone-frontend, with Python 3.10.

Backend

Navigate to backend folder:

cd evo2-backend

Install dependencies:

pip install -r requirements.txt

Modal setup:

modal setup

Run on Modal:

modal run main.py

Deploy backend:

modal deploy main.py

Frontend

Install dependencies:

cd evo2-frontend
npm i

Run:

npm run dev