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.

Running

Please see these docs for instructions on how to run this build yourself.

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.

Finalizing automated builds

To run a regional build, be sure to update the list of regions in config/nextstrain_config.yaml. You can run all builds in parallel with the following command.

snakemake --profile profiles/nextstrain all_regions

Or you can specify final or intermediate output files like so:

# subsampled regional focal
snakemake --profile profiles/nextstrain auspice/ncov_europe.json

# subsampled global
snakemake --profile profiles/nextstrain auspice/ncov_global.json

To update ordering/lat_longs after AWS download:

snakemake --touch --forceall --profile profiles/nextstrain
snakemake --profile profiles/nextstrain clean_export_regions
snakemake --profile profiles/nextstrain export_all_regions

When done adjusting lat-longs & orders, remember to run the following command to produce the final Auspice files.

snakemake --profile profiles/nextstrain all_regions