Merge pull request #202 from nextstrain/add-measles-dataset

Add measles dataset

data/nextstrain/collection.json

@@ -51,6 +51,8 @@
     "nextstrain/flu/h3n2/pa",
     "nextstrain/flu/h1n1pdm/pb2",
     "nextstrain/flu/h1n1pdm/pb1",
-    "nextstrain/flu/h3n2/pb2"
+    "nextstrain/flu/h3n2/pb2",
+    "nextstrain/measles",
+    "nextstrain/measles/N450/WHO-2012"
   ]
 }

data/nextstrain/measles/N450/WHO-2012/CHANGELOG.md

@@ -0,0 +1,3 @@
+## Unreleased
+
+Initial release.

data/nextstrain/measles/N450/WHO-2012/README.md

@@ -0,0 +1,32 @@
+# Measles dataset
+
+| Key               | Value                                                                                                                                                            |
+| ----------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| name           | Measles N450 (WHO-2012)    
+| authors           | [Nextstrain](https://nextstrain.org)                                            |
+| reference         | NC_001498.1                                                                                                                        |
+| workflow          | https://github.com/nextstrain/measles/tree/main/nextclade                                                                                     |
+| path              | `nextstrain/measles/N450/WHO-2012`                                                                                                                                  |
+
+
+## Scope of this dataset
+
+This dataset assigns genotypes to measles samples based on [criteria outlined by the WHO](https://www.who.int/publications/i/item/WER8709). 
+
+The WHO has defined 24 measles genotypes based on N gene and H gene sequences from 28 reference strains. For new measles samples, genotypes can be assigned based on genetic similarity to the reference strains at the "N450" region (a 450 bp region of the N gene). 
+
+The reference tree used in this dataset includes N450 sequences for the 28 reference strains, along with other representative strains for each genotype. 
+
+This dataset can be used to assign genotypes to any sequence that includes at least 400 bp of the N450 region, including whole genome sequences. Sequence data beyond the N450 region will be reported as an insertion in the Nextclade output.
+
+## Features
+
+This dataset supports:
+
+- Assignment of genotypes
+- Phylogenetic placement
+- Sequence quality control (QC)
+
+## What are Nextclade datasets
+
+Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html