This repository includes an example configuration file for running a Nextstrain analysis of SARS-CoV-2 genomes from GISAID for a specific country (South Africa). To make your own country-level analysis, edit this configuration file to change the country from "South Africa" to your country of choice.
View the tree from this analysis through Nextstrain's community interface. You can view trees hosted on GitHub with a URL like https://nextstrain.org/community/blab/ncov-africa@main/south-africa where blab is the organization, ncov-africa is the repository, main is the branch, and south-africa corresponds to a file in the repository named ncov-africa_south-africa.json. See the documentation for Nextstrain Community builds for more details.
Setup the Nextstrain software environment and download the ncov workflow. For example, to download the workflow you can run the following command.
git clone https://github.com/nextstrain/ncov.gitSelect data from GISAID for your country and for phylogenetic context.
Download these data files into your ncov/data/ directory.
For this analysis, we will use recent data from South Africa and the recent "nextregions" download for Africa.
Download this repository into the parent directory of the ncov workflow.
git clone https://github.com/blab/ncov-africa.gitChange directories to the ncov workflow.
cd ncov/Edit the workflow configuration for your country, as needed. For example, change instances of "south-africa" and "South Africa" to your country of interest.
open ../ncov-africa/builds.yamlDry-run the workflow (print commands without running anything).
nextstrain build . -j 4 -n -p --configfile ../ncov-africa/builds.yamlCreate a graph of the workflow.
nextstrain build . --configfile ../ncov-africa/builds.yaml --dag | dot -Tpdf > dag.pdfView a graph of the workflow.
open dag.pdfRun the workflow.
nextstrain build . -j 4 -p --configfile ../ncov-africa/builds.yamlView the resulting tree locally with Auspice.
nextstrain view auspice/Open the local Auspice server at http://localhost:4000/.