Update datasets with READMEs

nextclade/datasets/all/README.md

@@ -1,4 +1,4 @@
-# De dataset
+# Dengue dataset
 
 | Key  | Value  |
 | :-- | :-- |
@@ -11,7 +11,7 @@
 
 ## Scope of this dataset
 
-This dataset assigns serotype to dengue samples based on [criteria outlined by the WHO](https://pubmed.ncbi.nlm.nih.gov/26868382/) and tree placement nearest references [NC_001477.1 (DENV1)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001477.1), [NC_001474.2 (DENV2)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001474.2), [NC_001475.2 (DENV3)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001475.2), and [NC_002640.1 (DENV4)](https://www.ncbi.nlm.nih.gov/nuccore/NC_002640.1).
+This dataset assigns serotype (e.g. DENV1-DENV4) to dengue samples based on [criteria outlined by the WHO](https://pubmed.ncbi.nlm.nih.gov/26868382/) and tree placement nearest references [NC_001477.1 (DENV1)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001477.1), [NC_001474.2 (DENV2)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001474.2), [NC_001475.2 (DENV3)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001475.2), and [NC_002640.1 (DENV4)](https://www.ncbi.nlm.nih.gov/nuccore/NC_002640.1).
 
 ## Features
 

nextclade/datasets/denv1/README.md

@@ -1,8 +1,25 @@
-# Nextclade dataset for "UNKNOWN" (/Users/jchang3/github/nextstrain/dengue_branches/nextclade_assignment/nextclade_data/denv1)
+# Dengue virus DENV1 dataset
 
+| Key  | Value  |
+| :-- | :-- |
+| name  | Dengue virus DENV1 (genotype-level) |
+| authors | [Nextstrain](https://nextstrain.org) |
+| reference | NC_001477.1 |
+| workflow  | https://github.com/nextstrain/dengue/tree/main/nextclade  |
+| path  | `nextstrain/dengue/denv1` |
 
-## Dataset attributes
+## Scope of this dataset
 
-Nextclade dataset
+This dataset assigns DENV1 genotypes to dengue serotype 1 samples based on [curated reference strains by Sidney Bell](https://github.com/blab/dengue-antigenic-dynamics/blob/master/data/reference/strain_genotypes.tsv) from [Bell et al, 2019](https://elifesciences.org/articles/42496).
 
-Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
+## Features
+
+This dataset supports:
+
+- Assignment of serotypes
+- 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

nextclade/datasets/denv2/README.md

@@ -1,8 +1,26 @@
-# Nextclade dataset for "Dengue Virus"
+# Dengue virus DENV2 dataset
 
+| Key  | Value  |
+| :-- | :-- |
+| name  | Dengue virus DENV2 (genotype-level) |
+| authors | [Nextstrain](https://nextstrain.org) |
+| reference | NC_001474.2 |
+| workflow  | https://github.com/nextstrain/dengue/tree/main/nextclade  |
+| path  | `nextstrain/dengue/denv2` |
 
-## Dataset attributes
+## Scope of this dataset
 
-Nextclade dataset
+This dataset assigns DENV2 genotypes to dengue serotype 2 samples based on [curated reference strains by Sidney Bell](https://github.com/blab/dengue-antigenic-dynamics/blob/master/data/reference/strain_genotypes.tsv) from [Bell et al, 2019](https://elifesciences.org/articles/42496).
 
-Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
+
+## Features
+
+This dataset supports:
+
+- Assignment of serotypes
+- 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

nextclade/datasets/denv3/README.md

@@ -1,8 +1,25 @@
-# Nextclade dataset for "Dengue Virus"
+k# Dengue virus DENV3 dataset
 
+| Key  | Value  |
+| :-- | :-- |
+| name  | Dengue virus DENV3 (genotype-level) |
+| authors | [Nextstrain](https://nextstrain.org) |
+| reference | NC_001475.2 |
+| workflow  | https://github.com/nextstrain/dengue/tree/main/nextclade  |
+| path  | `nextstrain/dengue/denv3` |
 
-## Dataset attributes
+## Scope of this dataset
 
-Nextclade dataset
+This dataset assigns DENV3 genotypes to dengue serotype 3 samples based on [curated reference strains by Sidney Bell](https://github.com/blab/dengue-antigenic-dynamics/blob/master/data/reference/strain_genotypes.tsv) from [Bell et al, 2019](https://elifesciences.org/articles/42496).
 
-Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
+## Features
+
+This dataset supports:
+
+- Assignment of serotypes
+- 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

nextclade/datasets/denv4/README.md

@@ -1,8 +1,26 @@
-# Nextclade dataset for "Dengue Virus"
+# Dengue virus DENV4 dataset
 
+| Key  | Value  |
+| :-- | :-- |
+| name  | Dengue virus DENV4 (genotype-level) |
+| authors | [Nextstrain](https://nextstrain.org) |
+| reference | NC_002640.1 |
+| workflow  | https://github.com/nextstrain/dengue/tree/main/nextclade  |
+| path  | `nextstrain/dengue/denv4` |
 
-## Dataset attributes
+## Scope of this dataset
 
-Nextclade dataset
+This dataset assigns DENV4 genotypes to dengue serotype 4 samples based on [curated reference strains by Sidney Bell](https://github.com/blab/dengue-antigenic-dynamics/blob/master/data/reference/strain_genotypes.tsv) from [Bell et al, 2019](https://elifesciences.org/articles/42496).
 
-Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
+
+## Features
+
+This dataset supports:
+
+- Assignment of serotypes
+- 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