Latest alignment to Pathogen repo guide and add frequency panel #88
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This commit updates the `ingest` directory to match the latest version of the: https://github.com/nextstrain/pathogen-repo-guide/tree/b4001735fa55448f1426ff90cca93c667ca121ce/ingest
Since auspice automatically detects "authors" and we prefer the abbreviated authors list displayed, change "abbr_authors" to "authors" and "authors" to "full_authors". This matches the pathogen-repo-guide
To match the pathogen repo guide, change: * `genbank_accession` to `accession` * `genbank_accession_rev` to `accession_version` There should be a subsequent change in the phylogenetic workflow
To be more consistent with the pathogen-repo-guide and the ingest workflow
Use the combination of `accession` and `url` fields in the phylogenetic build. This change follows a similar change to the ingest workflow.
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Something is off in the frequency calculations. Here's a view from https://nextstrain.org/staging/dengue/trials/2024bfreq/dengue/all/genome?d=tree,frequencies&f_region=South%20America that just filters to South American sequences. I can mouse-over and clearly see a large number of samples from the last five years. However, none of these samples are showing up in the frequencies panel. 
You can see a similar issue without even filtering. It looks there's a single sample that's contributing to the KDE frequencies post 2020. 
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Compare measles example here that without normalizing frequencies you should have things sum to 100% without any filters in place: 
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Thank you! I was also expecting frequencies to sum up to 100%. The code changes to add frequencies panel are here, in case someone sees what's wrong faster than I can: I'm not entirely certain what is causing the empty regions:
I was mainly following frequency parameters for yellow-fever and measles but feel like I'm missing a nuance somewhere. |
Description of proposed changes
Since I was already in this repository to add the frequency panel, I decided to initiate an update to the workflow to align it with the latest version of the Pathogen Repo Guide.
Draft Frequencies Plot
Added frequencies plots from Actions run: https://github.com/nextstrain/dengue/actions/runs/12433607449
full genome frequencies:
E gene frequencies:
Feedback welcome
Related issue(s)
configtodefaults#77Checklist