From b692425b72c65cfe5ef36427b8c7777d84e73f73 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 13 Dec 2023 18:24:22 +0100 Subject: [PATCH 1/2] Add clade figures to SC2 readmes --- data/nextstrain/sars-cov-2/BA.2.86/README.md | 14 ++++++++++++++ data/nextstrain/sars-cov-2/BA.2/README.md | 14 ++++++++++++++ data/nextstrain/sars-cov-2/XBB/README.md | 14 ++++++++++++++ .../sars-cov-2/wuhan-hu-1/orfs/README.md | 14 ++++++++++++++ .../sars-cov-2/wuhan-hu-1/proteins/README.md | 14 ++++++++++++++ 5 files changed, 70 insertions(+) diff --git a/data/nextstrain/sars-cov-2/BA.2.86/README.md b/data/nextstrain/sars-cov-2/BA.2.86/README.md index 28d25e3b..a04b75b9 100644 --- a/data/nextstrain/sars-cov-2/BA.2.86/README.md +++ b/data/nextstrain/sars-cov-2/BA.2.86/README.md @@ -30,6 +30,20 @@ This dataset supports: - Phylogenetic placement - Calculation of ACE2 binding scores relative to BA.2.86 as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951) +## Nextstrain clades + +Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations. + +Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021. + +We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). + +Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)): + +![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg) + +Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/). + ## What are Nextclade datasets Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data/nextstrain/sars-cov-2/BA.2/README.md b/data/nextstrain/sars-cov-2/BA.2/README.md index c1d735ca..670168d2 100644 --- a/data/nextstrain/sars-cov-2/BA.2/README.md +++ b/data/nextstrain/sars-cov-2/BA.2/README.md @@ -31,6 +31,20 @@ This dataset supports: - Calculation of immune escape scores relative to BA.2 neutralizing antibodies as described in [Greaney et al. 2022](https://doi.org/10.1093/ve/veac021) - Calculation of ACE2 binding scores relative to BA.2 as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951) +## Nextstrain clades + +Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations. + +Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021. + +We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). + +Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)): + +![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg) + +Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/). + ## What are Nextclade datasets Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data/nextstrain/sars-cov-2/XBB/README.md b/data/nextstrain/sars-cov-2/XBB/README.md index de8afcf4..b84022a2 100644 --- a/data/nextstrain/sars-cov-2/XBB/README.md +++ b/data/nextstrain/sars-cov-2/XBB/README.md @@ -31,6 +31,20 @@ This dataset supports: - Calculation of immune escape scores relative to XBB neutralizing antibodies as described in [Greaney et al. 2022](https://doi.org/10.1093/ve/veac021) - Calculation of ACE2 binding scores relative to XBB as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951) +## Nextstrain clades + +Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations. + +Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021. + +We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). + +Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)): + +![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg) + +Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/). + ## What are Nextclade datasets Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/README.md b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/README.md index b7bec24c..3d8580c1 100644 --- a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/README.md +++ b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/README.md @@ -29,6 +29,20 @@ This dataset supports: - Sequence QC - Phylogenetic placement +## Nextstrain clades + +Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations. + +Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021. + +We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). + +Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)): + +![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg) + +Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/). + ## What are Nextclade datasets Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/README.md b/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/README.md index c6583490..8fa65553 100644 --- a/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/README.md +++ b/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/README.md @@ -31,6 +31,20 @@ This dataset supports: - Sequence QC - Phylogenetic placement +## Nextstrain clades + +Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations. + +Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021. + +We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). + +Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)): + +![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg) + +Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/). + ## What are Nextclade datasets Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html From b6807b0d0b66ce7b6bba831fd6ee2329607bb5d7 Mon Sep 17 00:00:00 2001 From: nextstrain-bot Date: Wed, 13 Dec 2023 17:25:50 +0000 Subject: [PATCH 2/2] chore: rebuild [skip ci] --- .../sars-cov-2/BA.2.86/unreleased/README.md | 14 ++++++++++++++ .../sars-cov-2/BA.2/unreleased/README.md | 14 ++++++++++++++ .../nextstrain/sars-cov-2/XBB/unreleased/README.md | 14 ++++++++++++++ .../wuhan-hu-1/orfs/unreleased/README.md | 14 ++++++++++++++ .../wuhan-hu-1/proteins/unreleased/README.md | 14 ++++++++++++++ 5 files changed, 70 insertions(+) diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/README.md b/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/README.md index 28d25e3b..a04b75b9 100644 --- a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/README.md +++ b/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/README.md @@ -30,6 +30,20 @@ This dataset supports: - Phylogenetic placement - Calculation of ACE2 binding scores relative to BA.2.86 as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951) +## Nextstrain clades + +Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations. + +Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021. + +We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). + +Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)): + +![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg) + +Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/). + ## What are Nextclade datasets Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/README.md b/data_output/nextstrain/sars-cov-2/BA.2/unreleased/README.md index c1d735ca..670168d2 100644 --- a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/README.md +++ b/data_output/nextstrain/sars-cov-2/BA.2/unreleased/README.md @@ -31,6 +31,20 @@ This dataset supports: - Calculation of immune escape scores relative to BA.2 neutralizing antibodies as described in [Greaney et al. 2022](https://doi.org/10.1093/ve/veac021) - Calculation of ACE2 binding scores relative to BA.2 as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951) +## Nextstrain clades + +Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations. + +Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021. + +We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). + +Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)): + +![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg) + +Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/). + ## What are Nextclade datasets Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/README.md b/data_output/nextstrain/sars-cov-2/XBB/unreleased/README.md index de8afcf4..b84022a2 100644 --- a/data_output/nextstrain/sars-cov-2/XBB/unreleased/README.md +++ b/data_output/nextstrain/sars-cov-2/XBB/unreleased/README.md @@ -31,6 +31,20 @@ This dataset supports: - Calculation of immune escape scores relative to XBB neutralizing antibodies as described in [Greaney et al. 2022](https://doi.org/10.1093/ve/veac021) - Calculation of ACE2 binding scores relative to XBB as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951) +## Nextstrain clades + +Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations. + +Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021. + +We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). + +Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)): + +![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg) + +Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/). + ## What are Nextclade datasets Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/README.md b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/README.md index b7bec24c..3d8580c1 100644 --- a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/README.md +++ b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/README.md @@ -29,6 +29,20 @@ This dataset supports: - Sequence QC - Phylogenetic placement +## Nextstrain clades + +Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations. + +Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021. + +We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). + +Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)): + +![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg) + +Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/). + ## What are Nextclade datasets Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/README.md b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/README.md index c6583490..8fa65553 100644 --- a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/README.md +++ b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/README.md @@ -31,6 +31,20 @@ This dataset supports: - Sequence QC - Phylogenetic placement +## Nextstrain clades + +Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations. + +Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021. + +We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). + +Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)): + +![Illustration of phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain](https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg) + +Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/). + ## What are Nextclade datasets Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html