EpiScore

Scoring for predicting spread of SARS-CoV-2 mutations

Installation

Using conda

The python environment can be configured with: conda env create -f environment.yml

Using docker

You can build the docker environment with docker build .

An example for running from docker can be found in run_docker.sh You will have to update CONTAINER_ID on the first line of the script to match the ID of the container you built. The comments within the script will make it clear where to update the input file, output directory, etc.

Obtaining input data

The input to this method is GISAID metadata. You can apply for access to GISAID here: https://www.gisaid.org/registration/register/

From the registered user landing page, you navigate to EpiCov -> Downloads -> Metadata

This should download a file named metadata_tsv_{date}.tar.xz

Untar this file. Inside you'll find metadata.tsv. This file is the input to the command below.

Usage

python forecasting.py [GISAID metadata file] [Output folder]

Output

A table of EpiScores and EpiScore components for each observed mutation