From a035ad1d612838a1634096b9eb83394f27d45f56 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 5 Jun 2024 16:17:50 -0700 Subject: [PATCH] Update datasets with READMEs --- nextclade/datasets/all/README.md | 4 ++-- nextclade/datasets/denv1/README.md | 25 +++++++++++++++++++++---- nextclade/datasets/denv2/README.md | 26 ++++++++++++++++++++++---- nextclade/datasets/denv3/README.md | 25 +++++++++++++++++++++---- nextclade/datasets/denv4/README.md | 26 ++++++++++++++++++++++---- 5 files changed, 88 insertions(+), 18 deletions(-) diff --git a/nextclade/datasets/all/README.md b/nextclade/datasets/all/README.md index affdf57a..3287dd8d 100644 --- a/nextclade/datasets/all/README.md +++ b/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 diff --git a/nextclade/datasets/denv1/README.md b/nextclade/datasets/denv1/README.md index e381574f..32e995a7 100644 --- a/nextclade/datasets/denv1/README.md +++ b/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 \ No newline at end of file diff --git a/nextclade/datasets/denv2/README.md b/nextclade/datasets/denv2/README.md index 964e8494..beeb41c0 100644 --- a/nextclade/datasets/denv2/README.md +++ b/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 \ No newline at end of file diff --git a/nextclade/datasets/denv3/README.md b/nextclade/datasets/denv3/README.md index 964e8494..696e5db5 100644 --- a/nextclade/datasets/denv3/README.md +++ b/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 \ No newline at end of file diff --git a/nextclade/datasets/denv4/README.md b/nextclade/datasets/denv4/README.md index 964e8494..d2d0d358 100644 --- a/nextclade/datasets/denv4/README.md +++ b/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 \ No newline at end of file