Include vaccine strains #23
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This commit adds strain and date annotations for 5 vaccine strains that all descend from Edmonston isolate collected in 1954. The Parks et al. paper describes these well. I purposely chose not to include location for these as I wanted the gray dot in the Auspice tree to make these look a bit different than wild-type isolates This also includes strain, date and location for Edmonston WT strain.
There's not enough genome data to warrant inclusion of month in the subsampling grouping. Also, by including month the subsampling was dropping a number of older samples that were only annotated by year. I noticed this in wanting to include the 1954 Edmonston related vaccine strains and they were getting filtered out with the previous "country year month" group-by.
Strain name is often not included in GenBank or is not very helpful. But still good to surface as metadata for modal. I particularly wanted this for the 1954 Edmonston-related vaccine strains. People know these by their strain names, certainly not their GenBank accessions.
joverlee521
reviewed
Apr 12, 2024
This swap to using --metadata-columns in augur export to surface strain, division and location.
kimandrews
approved these changes
Apr 12, 2024
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| export: | ||
| metadata_columns: "strain division location" |
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That sounds good to surface the strain names now. Eventually we should be able to pull more strain names from GenBank, after NCBI Datasets starts pulling the "strain" field, which is where most measles strain names are reported on GenBank (currently we are getting strain names from Genbank's "isolate" field, which NCBI Datasets does pull). NCBI says this is planned for sometime this year. This would also enable us to recover dates for some samples that have empty dates, since dates are part of the strain name.
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Excellent! Thanks for the context.
kimandrews
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Apr 19, 2024
Explicitly add vaccine strains to genome tree and N450 tree, following up on #23 These strains currently end up in the trees due to our subsampling parameters and lack of other sequences from 1954, but this commit explicitly adds them.
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Full genomes for Edmonston-related vaccine strains were present in the ingest dataset, but weren't making it to the final genome or N450 results due to getting filtered out from lack of
datemetadata. This PR surfaces these vaccine strains by:country yeargroup-by so that samples with just year metadata make it into the final build.straincoloring to provide proper descriptions of these 6 samples.I've just the entire pipeline locally and everything works as expected.
Results from running this branch are viewable at: