Please see the main Nextstrain docs for instructions for installing the Nextstrain bioinformatics pipeline (Augur) and visualization tools (Auspice).
In order to run the Nextstrain build you must provision
We've included a test set of sequences that are publicly available via Genbank as
Begin by copying the example data into the main data directory
cp example_data/sequences.fasta data/
Then, the entire build can be regenerated by running
with a local Nextstrain installation or by running
nextstrain build .
with a containerized Nextstrain installation.
The resulting output JSON at
auspice/ncov.json can be visualized by running
auspice view --datasetDir auspice or
nextstrain view auspice/ depending on local vs containerized installation.
This requires Augur version >=6.3.0, released Feb 13, 2020.