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It makes it easier to compare our trees with the Nextstrain tree and replicate some published analysis, e.g. Bloom et al.'s mutational spectra across variants.
These definitions are probably more s…
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This is a meta-issue to track the completion of the overall goal of creating and refining a Lassa build at nextstrain.org/lassa.
To launch build:
- https://github.com/nextstrain/lassa/issues/14
-…
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Extracted from priorities meeting notes; issue created to track progress.
Ticket assignment based on lead in notes.
## Related PRs
- https://github.com/nextstrain/ncov/pull/1029
- https://…
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Currently, CSS styles are applied using various approaches listed below with examples.
- Global defaults defined in [static-site/src/styles/globals.css](https://github.com/nextstrain/nextstrain.org…
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https://github.com/nextstrain/conda-base/blob/02cf82eee26e39b6772c2cdb47b7cca622bd3df0/.github/workflows/ci.yaml#L138
Expanding the above TODO into a GitHub issue.
Currently, pathogen CI only ru…
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We currently manually curate a [host_map.tsv](https://github.com/nextstrain/avian-flu/blob/0ddee36abda7f3831d2aa4a878d003866e7993af/ingest/build-configs/ncbi/defaults/host-map.tsv) for mapping specifi…
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Flagged [internally](https://support.nextstrain.org/agent/nextstrain/nextstrain/tickets/details/668036000007764001) by @rneher that the acknowledgements download does not include the GISAID isolate ID…
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Based on @victorlin's proposed solution in https://github.com/nextstrain/conda-base/issues/83
> In `nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml`, add an input to be passed to `jobs.b…
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Probably a simple approach to visually compare the backbones of the Viridian UShER tree and our pandemic-scale ARG is to leverage the Pango lineage roots, excluding the Pango recombinants. The Pango l…
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Brought up by @huddlej on [Slack](https://bedfordlab.slack.com/archives/C03KWDET9/p1724870542715349?thread_ts=1699914235.686809&cid=C03KWDET9) that OneDrive includes flat files. Ingesting the flat fil…