Nextclade build for Yellow Fever Virus (full genome)

Instructions

To run this build yourself, you will first need to install some dependencies. We provide a .yaml file you can use to set up a conda/mamba environment, e.g.:

micromamba env create -f environment.yaml
micromamba activate yellow-fever-virus

Next, create the directory structure expected by the workflow:

mkdir -p data/translations results/ out-dataset/

Following this, you can run the workflow using snakemake --cores <n> all, where you substitute <n> with the number of cores you want to allocate the run.

Visualising output

The generated tree can be viewed using auspice:

npx auspice view --datasetDir out-dataset/

Then open:

http://localhost:4000/tree

To run the dataset with example data, you can serve it locally and run nextclade:

npx serve --cors out-dataset -l 3000

Then open:

https://master.clades.nextstrain.org/?dataset-url=http://localhost:3000