Adding Frequencies Panel

Help and Getting Started
#1

I got a little lost on the documentation.

I really like the “frequencies” panel in the nextstrain builds, but I am not sure how to add it into my local build. I have a local build has sequences that are not in GISAID and are not even always SARS-CoV-2.

Just changing the auspice config file to include

"
“panels”: [
“tree”,
“map”,
“entropy”,
“frequencies”
],
"

didn’t magically make it appear, so there’s a rule that I’m missing somewhere.

What rule adds the information needed for the “frequencies” panel to appear?

If it helps, I used the zika tutorial snakefile as a template for my local builds.

#2

Hey Erin – there are two things needed for this to work:

  1. add “frequencies” to the panels in the JSON. It looks like you’ve done this correctly.

  2. Make sure a “tip-frequencies” JSON is available for auspice to fetch. The filename here should be the same as the main dataset JSON, but with _tip-frequencies added. For instance, these are the files behind nextstrain.org/flu/seasonal/yam/na/2y: https://data.nextstrain.org/flu_seasonal_yam_na_2y.json and http://data.nextstrain.org/flu_seasonal_yam_na_2y_tip-frequencies.json.

The creation of the tip-frequencies JSON is typically via augur frequencies (docs here). For an example, here’s the snakemake rule we use to create this for our SARS-CoV-2 builds.