Comments (3)
rneher
commented on July 19, 2024
1
I don't see a need for this outside of flu right now. So my suggestion would be to develop a clean and generic way in flu that can be moved to augur at a later point if need arises.
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huddlej
commented on July 19, 2024
There are two possible reasons I'd want to include this in augur. Even though those specific attributes are flu-specific, the way they are calculated is pathogen-independent. Placing this code in augur would also avoid duplication of code between my other flu repo and the seasonal flu repo.
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huddlej
commented on July 19, 2024
This is somewhat addressed by 8df9cf3, but we still need a non-epitope mask for NA (bhatt_nonepitope, perhaps) and a way of optionally displaying RBS mutations for just HA and not NA in auspice (there might already be a way of doing this that I'm not aware of).
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Related Issues (20)
- Example build not working. MissingRuleException HOT 6
- Unable to run nextstrain command under 'Quickstart with GISAID data' HOT 3
- Revisit deploy-private-nextflu Netlify CLI version pin
- Automate monthly reports
- Use Nextclade to assign clade labels in main phylogenetic workflow
- Export GISAID accessions from metadata into Auspice JSONs
- Add rules to the nextflu-private workflow to rename Auspice JSONs based on the build date and deploy the JSONs to the Nextstrain group
- Filter low-quality sequences by Nextclade QC status
- Integrating FASTA Sequence into Influenza A/H3N2 Evolution Analysis and Visualizing in Nextclade HOT 6
- Running issue nextstrain pipeline HOT 18
- Rename public nextstrain builds to `seasonal-flu`
- "Suffolk" in `lat_longs.tsv` points to somewhere unexpected HOT 1
- Automate deployment of private nextflu.org site
- Use metadata from NA segment in joined metadata when HA segment isn't available
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- Use a narrative template file to stub out a date-specific narrative for a given set of dated builds
- Use existing public 2y builds as “representative” trees in our reports
- Rename `master` to `main`
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