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Pyro models for SARS-CoV-2 analysis -- Reproducing analysis

Installation

Clone this repository

Clone this repository to ~/pyro-cov

Install nextclade

Depending on your platform do:

make install-nextalign-linux
make install-nextclade-linux

or

make install-nextalign
make install-nextclade

Install the package

pip install -e .[test]

Getting GISAID data

  1. Work with GISAID to get a data agreement.
  2. Create a directory ~/data/gisaid/
  3. Update pull_gisaid.sh file with your credentials and feed

Install dependencies

  1. conda install nodejs
  2. npm install --global @nextstrain/nextclade
  3. make update

Run vary holdout experiements

python mutrans.py --vary-holdout

Run backtesting experiments

./run_backtesting.py
``