nextclade-datasets

This directory is a Genspectrum-maintained nextclade server, created using the docs: https://github.com/nextstrain/nextclade_data/blob/master/docs/dataset-server-maintenance.md.

How to add new datasets?

Create a dataset following nextclade's instructions.
Update the index.json: this should include the details from each pathogen.json folder, additionally the index.json expects datasets to be versioned. For simplicity set version to unreleased and keep each dataset in a subdirectory called unreleased.
Zip the contents of the dataset into dataset.zip - this is what will be downloaded by nextclade and unzipped prior to use.

for i in {1..8}; do
    rm -rf dataset.zip
    cd seg$i/unreleased
    zip -r dataset.zip *
    cd -
done

Note that steps 2 and 3 are performed automatically by the CI when you create an official nextclade dataset, using the rebuild script.

Download H5N1 datasets as follows:

for i in {1..8}; do 
    nextclade_dataset_name=flu/h5n1/seg$i
    nextclade_dataset_server=https://raw.githubusercontent.com/genspectrum/nextclade-datasets/main/data
    nextclade3 dataset get --name $nextclade_dataset_name --server $nextclade_dataset_server --output-dir output$i
done