Nextstrain build for novel coronavirus SARS-CoV-2

Developer guide

Setup

Please see the main Nextstrain docs for instructions for installing the Nextstrain bioinformatics pipeline (Augur) and visualization tools (Auspice).

Data

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

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.

Running

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.