Start nextstrain¶

As with the ARTIC pipeline, nextstrain is also installed in a conda environment. Activate it with:

conda activate nextstrain

Make sure, the conda environment is active during the next steps.

Run the basic nextstrain worflow with:

cd ~/workdir/ncov/
snakemake --cores 14 --profile ./my_profiles/getting_started

Then start the auspice server:

cd ~/workdir/ncov
nextstrain view auspice/

And view the results in a browser with:

firefox http://127.0.0.1:4000

If you are done inspecting the results, terminate the auspice server with Ctrl+C .

We will now include our own data and recompute the analysis.

References¶