/ncov-kenya

SARS-CoV-2 Nexstrain build for Kenya

MIT LicenseMIT

SARS-CoV-2 build for Kenya

This repository includes an example configuration file for running a Nextstrain analysis of SARS-CoV-2 genomes from GISAID for Kenya.

Data GISAID

Sequence data downloaded from GISAID database and processed

open ../ncov-kenya/builds.yaml

Edit the Auspice configuration, setting the build_url and maintainers, as needed.

Run the analysis

Run the workflow.

nextstrain build . -j 4 -p --configfile ../ncov-kenya/builds.yaml

Inspect the analysis

View the resulting tree locally with Auspice.

nextstrain view auspice/

Open the local Auspice server at http://localhost:4000/.