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 ./data/sequences.fasta and ./data/metadata.tsv.
We've included a test set of sequences that are publicly available via Genbank as ./example_data/sequences.fasta.
API access to the evolutionary analysis that powers the visualization at nextstrain.org/ncov is available at http://data.nextstrain.org/ncov.json. Schema information here.
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
snakemake -p
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.