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nextstrain / measles

Nextstrain build for measles virus
https://nextstrain.org/measles
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Include frequencies for N450 build #42

Closed trvrb closed 3 days ago

trvrb commented 1 week ago

This commit produces tip-frequencies JSON files for both N450 and genome analyses, but only displays frequencies panel for N450.

Start date of 2000 and end date of –6 months were chosen based on data availability. I increased bandwidth by about 2.5x to account for data quantity relative to temporal spread (compared to the 2y flu-like defaults).

Generally, I think it's quite useful to display frequencies once we have:

  1. A decent amount of sampling (with 3000 sequences the N450 build is good for this)
  2. A suitable granularity clade to display (MeV genotype works for this)

You can see output of running this PR here: https://nextstrain.org/staging/measles/frequencies/N450

Screenshot 2024-06-28 at 3 08 36 PM

There are some nice interactions, like seeing how restricted genotypes are in Africa vs Asia.

I've tagged @joverlee521 here as reviewer as well because I wasn't sure how frequencies should fit into the https://github.com/nextstrain/pathogen-repo-guide. I chose to add the rule to annotate_phylogeny.smk, which seems most suitable, but it's not really annotating the tree and could be it's own frequencies.smk file. Also, I chose to output to results/tip_frequencies.json and then copy this file to auspice/ under export.smk, but this copying could be thought of as extraneous.

joverlee521 commented 1 week ago

I've tagged @joverlee521 here as reviewer as well because I wasn't sure how frequencies should fit into the https://github.com/nextstrain/pathogen-repo-guide. I chose to add the rule to annotate_phylogeny.smk, which seems most suitable, but it's not really annotating the tree and could be it's own frequencies.smk file. Also, I chose to output to results/tip_frequencies.json and then copy this file to auspice/ under export.smk, but this copying could be thought of as extraneous.

The pathogen-repo-guide currently suggests augur frequencies as part of the export.smk with the thought that it can output directly to the exported auspice/ directory 😄

trvrb commented 1 week ago

Ah! I missed this. This makes as much (if not more) sense to me as including it in annotate_phylogeny.smk. I'll update the PR.