This repo describes how to conduct the phylogenetic analysis described in the manuscript. You will also find figures and additional scripts that we used for parsing data and making figures.
To reproduce this analysis you'll need to have Nextstrain installed. Documentation on installing Nextstrain is available here.
This analysis also makes use of the Nextstrain team's ncov analysis repo, which you can find here. We recommend cloning this repo to your local machine and running the analysis within that repo (this will ensure all software components are up-to-date with the Nexstrain team's ncov builds).
The Nextstrain ncov builds use "profiles". You'll see in this repo that there is a directory called my_profiles, and within that directory there is another directory called humboldt. You'll want to move the humboldt directory over the the my_profiles directory within the nextstrain/ncov repo.
Once you have conda installed you can create the environment by running
conda env create -f humboldt-analysis-env.yaml within the top level directory of this repo.
Then, to load the environment run
conda activate humboldt-analysis
To open the jupyter notebooks you can run
jupyter notebook analysis-scripts/<notebook_name> within the top level directory of this repo.
To run the additional scripts in analysis-scripts you'll want to create a new conda environment from our environment file. If you do not already have conda installed you can find install directions here.