Add lineages coloring from https://dengue-lineages.org/ #93
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genehack
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Feb 24, 2025
joverlee521
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Totally support using existing community Nextclade datasets developed by those maintaining the dengue lineage system! As I've said in our discussions, I'm slightly worried that the community Nextclade datasets might not be maintained indefinitely, but we can tackle that when/if the time comes.
I only left a few non-blocking comments from a high level review.
Co-authored-by: Jover Lee <[email protected]>
Callapse both merge rules into one merge rule since augur merge works for multiple files. Drop an unused parameter.
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Description of proposed changes
This PR updates the dengue lineages to match https://dengue-lineages.org in response to various feedback including a slack message and various issues. Please see the following issue for further context:
The trees with updated lineage designations have been pushed to a staged site, linked in the table below as a convenience to PR reviewers.
See the below staged builds for the Verity Hill, 2024 lineage coloring:
Metadata with new columns "genotype", "major_lineage", and "minor_lineage" available at: https://data.nextstrain.org/files/workflows/dengue/trials/20250214hill/metadata_all.tsv.zst
dengue-lineages.org displays lineages using distinct colors for Genotype, Major, and Minor lineages, as illustrated in the diagram below with dengue 3 as an example:
I have implemented a similar distinct lineage color scheme in our tree visualization, also showing dengue 3 below as an example:
Related issue(s)
Checklist
[edit: added on 2025-02-18, after emailing Grubaugh et al]
Results:
[edit: added on 2025-02-20
Several of us investigated the mismatch for OK040058 (
4II_A.1vs1I_B). After some digging, it turns out version 1 classified as a dengue 4 sequence and version 2 classified as a a dengue 1 sequence.Validate lineage calls against references listed in https://github.com/DENV-lineages/lineages-paper