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feat(data): full-genome yellow fever virus#453

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maverbiest wants to merge 15 commits into
nextstrain:masterfrom
maverbiest:yellow-fever-virus
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feat(data): full-genome yellow fever virus#453
maverbiest wants to merge 15 commits into
nextstrain:masterfrom
maverbiest:yellow-fever-virus

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@maverbiest
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@maverbiest maverbiest commented May 22, 2026

Description of proposed changes

This PR adds a nextclade dataset built using full-genome sequences available on NCBI under /data/community/pathoplexus/yellow-fever-virus. We use this dataset for a linkout from Pathoplexus to provide a visual representation of where selected sequences fall in the genomic context of existing YFV sequences. The workflow used to generate the dataset is available in the Hodcroft Lab GitHub.

Any feedback and suggestions for improvements would be welcome, both on this PR and on the workflow used to generate the dataset.

Thank you very much!

Preview

https://clades.nextstrain.org/?dataset-server=gh:maverbiest/nextclade_data@yellow-fever-virus@/data_output&dataset-name=community/pathoplexus/yellow-fever-virus

Checklist

  • Check if changes affect downstream workflows which depend on this dataset. For instance, Nextstrain ingest workflows may break if clade nomenclature changes. Consider fixing those workflows or making an issue at least.

Comment thread data/community/pathoplexus/yellow-fever-virus/README.md Outdated
Comment thread data/community/pathoplexus/yellow-fever-virus/README.md Outdated
Comment thread data/community/pathoplexus/yellow-fever-virus/README.md
Comment thread data/community/pathoplexus/yellow-fever-virus/README.md
Comment thread data/community/pathoplexus/yellow-fever-virus/README.md Outdated
@corneliusroemer
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corneliusroemer commented May 22, 2026

I've added a preview link to the PR description

Maybe worth noting that the ref seq here is different from the other dataset as well.

Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com>
Comment thread data/community/pathoplexus/yellow-fever-virus/pathogen.json Outdated
maverbiest and others added 2 commits May 24, 2026 20:00
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2 participants