From 18597bb71c1d45d885db57ff1687e818403cceda Mon Sep 17 00:00:00 2001 From: Richard Neher Date: Mon, 16 Dec 2024 21:01:34 +0100 Subject: [PATCH 1/4] flu: add additional H1/HA subclade proposal --- data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md | 3 ++- data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json | 2 +- data/nextstrain/flu/h1n1pdm/ha/MW626062/CHANGELOG.md | 3 ++- data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json | 2 +- 4 files changed, 6 insertions(+), 4 deletions(-) diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md b/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md index 5da5bb92..8c5305ff 100644 --- a/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md +++ b/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md @@ -1,5 +1,6 @@ ## Unreleased - - include subclade proposals for C.1.9.a/b/c + + - add subclade proposals C.1.9.a/b/c/d ## 2024-11-27T02:51:00Z diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json b/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json index 69c25c55..eb8dddbc 100644 --- a/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json +++ b/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Nextclade reference tree for Influenza type:h1n1pdm segment:ha with root CY121680 built on 2024-12-14", "updated": "2024-12-14", "build_url": "https://github.com/nextstrain/seasonal-flu", "data_provenance": [{"name": "GISAID"}], "maintainers": [{"name": "Nextstrain team", "url": "https://nextstrain.org"}], "display_defaults": {"color_by": "subclade", "distance_measure": "div", "branch_label": "subclade"}, "genome_annotations": {"HA1": {"end": 1052, "seqid": "dataset_config/h1n1pdm/ha/CY121680/annotation.gff", "start": 72, "strand": "+", "type": "gene"}, "HA2": {"end": 1718, "seqid": "dataset_config/h1n1pdm/ha/CY121680/annotation.gff", "start": 1053, "strand": "+", "type": "gene"}, "SigPep": {"end": 71, "seqid": "dataset_config/h1n1pdm/ha/CY121680/annotation.gff", "start": 21, "strand": "+", "type": "gene"}, "nuc": {"end": 1752, "start": 1, "strand": "+", "type": "source"}}, "colorings": [{"key": "clade_membership", "title": "Clade", "type": "categorical"}, {"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "subclade", "title": "Subclade", "type": "categorical"}, {"key": "short-clade", "title": "short-clade", "type": "categorical"}, {"key": "proposedSubclade", "title": "Subclade proposals", "type": "categorical"}, {"key": "strain", "title": "strain", "type": "categorical"}, {"key": "region", "title": "Region", "type": "categorical", "scale": [["China", "#4042C7"], ["Southeast Asia", "#4274CE"], ["South Asia", "#5199B7"], ["Japan Korea", "#69B091"], ["Oceania", "#88BB6C"], ["West Asia", "#ADBD51"], ["Africa", "#CEB541"], ["Europe", "#E39B39"], ["South America", "#E56C2F"], ["North America", "#DC2F24"]]}, {"key": "country", "title": "Country", "type": "categorical"}, {"key": "date", "title": "Sample Date", "type": "ordinal"}, {"key": "gisaid_epi_isl", "title": "gisaid_epi_isl", "type": "categorical"}, {"key": "accession_ha", "title": "accession_ha", "type": "categorical"}], "filters": ["region", "country", "clade_membership", "subclade"], "panels": ["tree", "entropy"], "extensions": {"nextclade": {"clade_node_attrs": [{"name": "short-clade", "displayName": "short-clade", "description": ""}, {"name": "subclade", "displayName": "Subclade", "description": "Experimental fine-grained subclade annotation."}, {"name": "proposedSubclade", "displayName": "Proposed subclade", "description": "Includes proposals of new subclades. 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{}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ No newline at end of file From f8aba3d9eb14fddd80835bee932fac428159f700 Mon Sep 17 00:00:00 2001 From: nextstrain-bot Date: Mon, 16 Dec 2024 20:17:27 +0000 Subject: [PATCH 2/4] chore: rebuild [skip ci] --- data_output/index.json | 2 +- .../ha/CY121680/unreleased/CHANGELOG.md | 3 ++- .../ha/CY121680/unreleased/dataset.zip | Bin 1206083 -> 1206078 bytes .../h1n1pdm/ha/CY121680/unreleased/tree.json | 2 +- .../ha/MW626062/unreleased/CHANGELOG.md | 3 ++- .../ha/MW626062/unreleased/dataset.zip | Bin 1188770 -> 1188802 bytes .../h1n1pdm/ha/MW626062/unreleased/tree.json | 2 +- 7 files changed, 7 insertions(+), 5 deletions(-) diff --git a/data_output/index.json b/data_output/index.json index 0b0058ec..11321776 100644 --- a/data_output/index.json +++ b/data_output/index.json @@ -1004,7 +1004,7 @@ "customClades": { "short-clade": 16, "subclade": 22, - "proposedSubclade": 25 + "proposedSubclade": 26 }, "qc": [ "privateMutations", diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md index 5da5bb92..8c5305ff 100644 --- a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md +++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md @@ -1,5 +1,6 @@ ## Unreleased - - include subclade proposals for C.1.9.a/b/c + + - add subclade proposals C.1.9.a/b/c/d ## 2024-11-27T02:51:00Z diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/dataset.zip b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/dataset.zip index e72afde0b5be37382f01e872cd89b7dc52172d72..753806b35d80e5d0e9be140d3f71efad7172a1b7 100644 GIT binary patch literal 1206078 zcmeFaO>>)Bnx>bIp72a5?64g%F>5qy(N!~&NB|^A=GYy7~QV@pawj1qhM=2#}COsR&WP!FkVl z&hy;Q*E#3?z&Bs~*}wSLAC=difApXKuRr@w|I5Gn=p+CCS5$6)zV+nMXJ3B(=;6z~ zU;eW8H%G^v!%q98vv==a?Ln=*w^utkeZG6x-s{v}9rs@KPTGejwe5%Xhno-E%g>j0 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["C1659T"]}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ No newline at end of file diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md index 0693cc01..054a276f 100644 --- a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md +++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md @@ -1,5 +1,6 @@ ## Unreleased - - include subclade proposals for C.1.9.a/b/c + + - add subclade proposals C.1.9.a/b/c/d ## 2024-11-27T02:51:00Z diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/dataset.zip b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/dataset.zip index 18cbafa69bd6c57a58519faa3371f5412a21aeae..9547c26177231fadc03478d068c9318cf4633d5d 100644 GIT binary patch literal 1188802 zcmeFa+j3i3nxL1CX?t86JM4>z3EwyZ&ARBSnWTvGA;<0rB&A}ivr?%_v9r1-Lsmm1 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a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/tree.json +++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Nextclade reference tree for Influenza type:h1n1pdm segment:ha with root MW626062 built on 2024-12-14", "updated": "2024-12-14", "build_url": "https://github.com/nextstrain/seasonal-flu", "data_provenance": [{"name": "GISAID"}], "maintainers": [{"name": "Nextstrain team", "url": "https://nextstrain.org"}], "display_defaults": {"color_by": "subclade", "distance_measure": "div", "branch_label": "subclade"}, "genome_annotations": {"HA1": {"end": 1052, "seqid": "dataset_config/h1n1pdm/ha/MW626062/annotation.gff", "start": 72, "strand": "+", "type": "gene"}, "HA2": {"end": 1718, "seqid": "dataset_config/h1n1pdm/ha/MW626062/annotation.gff", "start": 1053, "strand": "+", "type": "gene"}, "SigPep": {"end": 71, "seqid": "dataset_config/h1n1pdm/ha/MW626062/annotation.gff", "start": 21, "strand": "+", 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{}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ No newline at end of file From 94503e7b8b1a178d21b7793432e06bd144913936 Mon Sep 17 00:00:00 2001 From: Richard Neher Date: Sat, 4 Jan 2025 17:06:49 +0100 Subject: [PATCH 3/4] flu: include additional proposals --- data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md | 4 +++- data/nextstrain/flu/h3n2/ha/CY163680/tree.json | 2 +- data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md | 3 ++- data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json | 2 +- data/nextstrain/flu/h3n2/na/EPI1857215/CHANGELOG.md | 5 +++++ data/nextstrain/flu/h3n2/na/EPI1857215/tree.json | 2 +- 6 files changed, 13 insertions(+), 5 deletions(-) diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md b/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md index 3a4229d6..2468b74d 100644 --- a/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md +++ b/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md @@ -1,5 +1,7 @@ ## Unreleased - - include 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a/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md +++ b/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md @@ -1,5 +1,6 @@ ## Unreleased - - include subclade proposals for J.2.a/b/c + + - include subclade proposals for J.2.a/b/c/d/e ## 2024-11-27T02:51:00Z diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json index de09d60e..dbbd4120 100644 --- a/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json +++ b/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Nextclade reference tree for Influenza type:h3n2 segment:ha with root EPI1857216 built on 2024-12-14", "updated": "2024-12-14", "build_url": "https://github.com/nextstrain/seasonal-flu", "data_provenance": [{"name": "GISAID"}], "maintainers": [{"name": "Nextstrain team", "url": "https://nextstrain.org"}], "display_defaults": {"color_by": "subclade", "distance_measure": "div", "branch_label": "subclade"}, "genome_annotations": 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a/data/nextstrain/flu/h3n2/na/EPI1857215/CHANGELOG.md b/data/nextstrain/flu/h3n2/na/EPI1857215/CHANGELOG.md index e5d8f41f..49999ee1 100644 --- a/data/nextstrain/flu/h3n2/na/EPI1857215/CHANGELOG.md +++ b/data/nextstrain/flu/h3n2/na/EPI1857215/CHANGELOG.md @@ -1,3 +1,8 @@ +## Unreleased + + - update reference tree + + ## 2024-11-05T09:19:52Z - update reference trees diff --git a/data/nextstrain/flu/h3n2/na/EPI1857215/tree.json b/data/nextstrain/flu/h3n2/na/EPI1857215/tree.json index e2676136..309abb60 100644 --- a/data/nextstrain/flu/h3n2/na/EPI1857215/tree.json +++ b/data/nextstrain/flu/h3n2/na/EPI1857215/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Nextclade reference tree for Influenza type:h3n2 segment:na with root EPI1857215 built on 2024-11-03", "updated": "2024-11-03", "build_url": "https://github.com/nextstrain/seasonal-flu", "data_provenance": [{"name": "GISAID"}], "maintainers": [{"name": "Nextstrain team", "url": "https://nextstrain.org"}], "display_defaults": 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"A/StPetersburg/RII-7682S/2023"}}, "branch_attrs": {"mutations": {}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ No newline at end of file From eb6a9082363dd85ebba205ddb2de044d1cfe52a9 Mon Sep 17 00:00:00 2001 From: nextstrain-bot Date: Sat, 4 Jan 2025 16:08:10 +0000 Subject: [PATCH 4/4] chore: rebuild [skip ci] --- data_output/index.json | 26 +- .../h3n2/ha/CY163680/unreleased/CHANGELOG.md | 4 +- .../h3n2/ha/CY163680/unreleased/dataset.zip | Bin 1410314 -> 1740378 bytes .../flu/h3n2/ha/CY163680/unreleased/tree.json | 2 +- .../ha/EPI1857216/unreleased/CHANGELOG.md | 3 +- .../h3n2/ha/EPI1857216/unreleased/dataset.zip | Bin 1515676 -> 1847720 bytes .../h3n2/ha/EPI1857216/unreleased/tree.json | 2 +- .../na/EPI1857215/unreleased/CHANGELOG.md | 21 + .../h3n2/na/EPI1857215/unreleased/README.md | 35 + .../h3n2/na/EPI1857215/unreleased/dataset.zip | Bin 0 -> 1138927 bytes .../unreleased/genome_annotation.gff3 | 4 + .../na/EPI1857215/unreleased/pathogen.json | 122 ++ .../na/EPI1857215/unreleased/reference.fasta | 2 + .../na/EPI1857215/unreleased/sequences.fasta | 1300 +++++++++++++++++ .../h3n2/na/EPI1857215/unreleased/tree.json | 1 + 15 files changed, 1508 insertions(+), 14 deletions(-) create mode 100644 data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/CHANGELOG.md create mode 100644 data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/README.md create mode 100644 data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/dataset.zip create mode 100644 data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/genome_annotation.gff3 create mode 100644 data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/pathogen.json create mode 100644 data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/reference.fasta create mode 100644 data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/sequences.fasta create mode 100644 data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/tree.json diff --git a/data_output/index.json b/data_output/index.json index 11321776..2920b150 100644 --- a/data_output/index.json +++ b/data_output/index.json @@ -1219,11 +1219,11 @@ "treeJson": "tree.json" }, "capabilities": { - "clades": 36, + "clades": 37, "customClades": { - "subclade": 44, - "short-clade": 36, - "proposedSubclade": 47 + "subclade": 45, + "short-clade": 37, + "proposedSubclade": 50 }, "qc": [ "privateMutations", @@ -1346,11 +1346,11 @@ "treeJson": "tree.json" }, "capabilities": { - "clades": 36, + "clades": 37, "customClades": { - "subclade": 44, - "short-clade": 36, - "proposedSubclade": 47 + "subclade": 45, + "short-clade": 37, + "proposedSubclade": 50 }, "qc": [ "privateMutations", @@ -1496,6 +1496,13 @@ ] }, "versions": [ + { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + }, { "updatedAt": "2024-11-05T09:19:52Z", "tag": "2024-11-05--09-19-52Z", @@ -1522,8 +1529,7 @@ } ], "version": { - "updatedAt": "2024-11-05T09:19:52Z", - "tag": "2024-11-05--09-19-52Z", + "tag": "unreleased", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md index 3a4229d6..2468b74d 100644 --- a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md +++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md @@ -1,5 +1,7 @@ ## Unreleased - - include subclade proposals for J.2.a/b/c + + - include subclade proposals for J.2.a/b/c/d/e + ## 2024-11-27T02:51:00Z diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/dataset.zip 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