Nextstrain Instance: the transmission of Delta variant in the greater Houston area

Use Git to download a copy of the ncov repository containing the workflow.

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

Change directory to the ncov directory:

cd ncov

Download this repository into a new subdirectory of ncov called deltaInGreaterHoustonArea:

git clone https://github.com/leke-lyu/deltaInGreaterHoustonArea.git

Replace the lat_longs.tsv:

rm defaults/lat_longs.tsv
cp deltaInGreaterHoustonArea/lat_longs.tsv defaults/

From within the ncov directory, run the workflow using a configuration file provided in the tutorial directory:

nextstrain build . --configfile deltaInGreaterHoustonArea/builds.yaml 

Visualize the results in here.