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Docs: Add description of the different lineage color options
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j23414 committed Feb 26, 2025
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Expand Up @@ -13,4 +13,26 @@ We curate sequence data and metadata from NCBI as starting point for our analyse
* [data.nextstrain.org/files/workflows/dengue/sequences_denv4.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/sequences_denv4.fasta.zst)
* [data.nextstrain.org/files/workflows/dengue/metadata_denv4.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/metadata_denv4.tsv.zst)

For more information about the dengue lineage system, to submit questions, or lineage proposals; please visit [dengue-lineages.org](https://dengue-lineages.org/).

### Lineage coloring

There are up to six different lineage coloring options available depending on the source of data:

**Based on a Nextclade call against [community/v-gen-lab/dengue datasets](https://github.com/nextstrain/nextclade_data/tree/master/data/community/v-gen-lab/dengue).**

The lineage color options are split into levels of detail, with an example shown beside each level:

* **Genotype (Nextclade):** 3III
* **Major Lineage (Nextclade):** 3III_B
* **Minor Lineage (Nextclade):** 3III_B.3.2

For more information about the dengue lineage system please visit [dengue-lineages.org](https://dengue-lineages.org/).

**Based on NCBI GenBank metadata**

* **Serotype (GenBank metadata):** denv1 to denv4

**Based on Augur clade assignment (`clade_membership`)**
_(Only available for genome trees, not gene trees)_
* **Serotype (Nextstrain):** DENV1 – DENV4, annotated only on the "all" tree
* **Genotype (Nextstrain):** such as DENV3/III _(equivalent to 3III in "Genotype (Nextclade)")_, annotated only on the serotype-specific trees.

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