Kenya-specific SARS-CoV-2 Nextstrain analysis

Get the workflow

Download the ncov workflow.

git clone https://github.com/nextstrain/ncov.git
cd ncov/

This directory contains the logic to run a Nextstrain analysis for SARS-CoV-2 based on a workflow build configuration you provide.

Get the workflow build configuration

Download the workflow build configuration into the ncov/ workflow directory.

git clone https://github.com/blab/ncov-kenya.git .

All configuration files for the Kenya workflow live in the resulting ncov-kenya/ directory.

Download data

Follow instructions to curate data from GISAID search and downloads. Specifically, search for "Africa / Kenya" in the search interface (checking the additional filters of "Complete", "Low coverage excluded", and "Collection date complete") and download the "Africa" bundle from the "nextregions" downloads on GISAID. Save the Kenya data to the ncov/ directory in the data/ subdirectory as kenya.tar. Compress the Kenyan data with gzip data/kenya.tar. Save the Africa nextregions file to the ncov/data/ directory as africa.tar.gz.

Alternately, if there are too many records to use GISAID's search interface, curate Kenya-specific data from the full GISAID database as described in this tutorial.

Run the workflow

Run the workflow with the Nextstrain CLI (or Snakemake, if you prefer), specifying the build configuration file in the ncov-kenya/ directory.

nextstrain build . --cores 4 -p --configfile ncov-kenya/builds_kenya.yaml

View the analysis output

View the analysis output locally by running the Nextstrain CLI (or Auspice, if you prefer) and navigating to the corresponding server address in your browser.