Merge pull request #71 from nextstrain/update-flu

update flu datasets and fix B/vic annotation

CHANGELOG.md

@@ -1,5 +1,15 @@
 # CHANGELOG
 
+## 2023-04-02
+
+### New dataset version (tag `2023-04-02T12:00:00Z`)
+
+#### Influenza virus datasets
+
+All Influenza virus datasets were updated with more recent sequences. The trees now include more older reference viruses for more robust designation of older clades.
+The B/Vic annotation of the HA segment was fixed -- it was previously off by 3 nucleotides resulting in amino acid numbering being off by one.
+
+
 ## 2023-03-28
 
 ### Internal

data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/genemap.gff

@@ -0,0 +1,5 @@
+##gff-version 3
+##sequence-region CY121680.1 1 1752
+CY121680.1	feature	gene	21	71	.	+	.	gene_name="SigPep"
+CY121680.1	feature	gene	72	1052	.	+	.	gene_name="HA1"
+CY121680.1	feature	gene	1053	1718	.	+	.	gene_name="HA2"

data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/primers.csv

@@ -0,0 +1 @@
+Country (Institute),Target,Oligonucleotide,Sequence

data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/qc.json

@@ -0,0 +1,33 @@
+{
+  "schemaVersion": "1.2.0",
+  "privateMutations": {
+    "enabled": true,
+    "typical": 5,
+    "cutoff": 15,
+    "weightLabeledSubstitutions": 2,
+    "weightReversionSubstitutions": 1,
+    "weightUnlabeledSubstitutions": 1
+  },
+  "missingData": {
+    "enabled": false,
+    "missingDataThreshold": 100,
+    "scoreBias": 10
+  },
+  "snpClusters": {
+    "enabled": false,
+    "windowSize": 100,
+    "clusterCutOff": 5,
+    "scoreWeight": 50
+  },
+  "mixedSites": {
+    "enabled": true,
+    "mixedSitesThreshold": 4
+  },
+  "frameShifts": {
+    "enabled": true
+  },
+  "stopCodons": {
+    "enabled": true,
+    "ignoredStopCodons": []
+  }
+}

data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/reference.fasta

@@ -0,0 +1,2 @@
+>CY121680.1 Influenza A virus (A/California/07/2009(H1N1)) hemagglutinin (HA) gene, complete cds
+GGAAAACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCGAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAAAACAC

data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/tag.json

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+{
+  "tag": "2023-04-02T12:00:00Z",
+  "comment": "Updated tree",
+  "compatibility": {
+    "nextcladeCli": {
+      "min": "1.3.0",
+      "max": null
+    },
+    "nextcladeWeb": {
+      "min": "1.6.0",
+      "max": null
+    }
+  },
+  "enabled": true,
+  "files": {
+    "geneMap": "genemap.gff",
+    "primers": "primers.csv",
+    "qc": "qc.json",
+    "reference": "reference.fasta",
+    "sequences": "sequences.fasta",
+    "tree": "tree.json",
+    "virusPropertiesJson": "virus_properties.json"
+  },
+  "metadata": {}
+}