In order to run the analysis yourself, you need to select all on GISAID, download and then select Input for the Augur pipeline.

Put the downloaded .tar file into the data folder.

Install Conda from https://www.anaconda.com/products/individual

Create a new environment with conda create -name ncov_simplest and conda activate ncov_simplest

Install mamba conda install mamba

Install nextclade and augur mamba install nextclade and mamba install python=3.9 augur

Downgrade bcbio mamba install bcbio-gff=0.6.7

Then run Snakemake with snakemake build -c0.

The resulting auspice.json will be in the folder auspice.