newcastle: initial import

data/nextstrain/collection.json

@@ -101,6 +101,8 @@
     "nextstrain/flu/h2n2/ha",
     "nextstrain/flu/h2n2/na",
     "nextstrain/flu/h2n2/mp",
-    "nextstrain/flu/h2n2/ns"
+    "nextstrain/flu/h2n2/ns",
+    "nextstrain/ndv/class-2/NC_075404",
+    "nextstrain/ndv/class-1/AB524405"
   ]
 }

data/nextstrain/ndv/class-1/AB524405/CHANGELOG.md

@@ -0,0 +1,4 @@
+## Unreleased
+
+ - initial release of the draft NDV class 1 dataset
+ - the class 2 reference NC_075404 is included in the reference tree as an outgroup, so that class 2 sequences attach to it and are reported as `class 2` instead of being placed inside the class 1 diversity

data/nextstrain/ndv/class-1/AB524405/README.md

@@ -0,0 +1,24 @@
+# Newcastle disease virus class 1 - All Genotypes with Reference Genome AB524405
+
+| Key                    | Value                                                                                                               |
+| ---------------------- | --------------------------------------------------------------------------------------------------------------------|
+| authors                | [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org)                                          |
+| data source            | Genbank, [NDV_Sequence_Datasets](https://github.com/NDVconsortium/NDV_Sequence_Datasets/)                             |
+| workflow               | [github.com/nextstrain/newcastle-disease-virus](https://github.com/nextstrain/newcastle-disease-virus)                |
+| nextclade dataset path | nextstrain/ndv/class-1/AB524405                                                                                      |
+| reference              | AB524405                                                                                                             |
+| genotype nomenclature  | [Dimitrov et al, 2019](https://doi.org/10.1016/j.meegid.2019.103917), as curated in [NDV_Sequence_Datasets](https://github.com/NDVconsortium/NDV_Sequence_Datasets/) |
+
+
+## Scope of this dataset
+This dataset covers class 1 of Newcastle disease virus (avian orthoavulavirus 1) and uses reference sequence [AB524405](https://www.ncbi.nlm.nih.gov/nuccore/AB524405.1/), the 15198 nt complete genome of goose/Alaska/415/91. The reference tree is built from the curated class 1 genomes of the NDV consortium sequence set, sampled between 1991 and 2020, and covers genotypes 1.1.1, 1.1.2 and 1.2. The class 1 part of the tree is mid-point rooted; it hangs, together with the class 2 outgroup described below, off a root that represents the common ancestor of the two classes.
+
+**Note: class 1 and class 2 are two separate datasets, built from different references and with separate genotype nomenclatures. Class 1 viruses are 15198 nt and class 2 viruses 15186 nt, but the two classes are close enough that a sequence of either class aligns against either reference. The class 2 reference [NC_075404](https://www.ncbi.nlm.nih.gov/nuccore/NC_075404.1/) is therefore part of this reference tree, as an outgroup: a class 2 sequence attaches to it rather than being placed somewhere inside the class 1 diversity, and is reported as `class 2` with no genotype. Run such a sequence against the [class 2 dataset](../class2) to get a genotype for it.**
+
+The reference itself (annotated as lineage 6 in GenBank, under the pre-2019 class 1 nomenclature) carries no genotype assignment in the curated set.
+
+### Features
+This dataset supports:
+ - Assignment to the unified genotype nomenclature proposed by [Dimitrov et al, 2019](https://doi.org/10.1016/j.meegid.2019.103917), based on the 2022 release of the NDV consortium sequence set. A node is labelled with a genotype only when every sequence below it carries that genotype; everything else is reported as `unclassified`.
+ - Phylogenetic placement
+ - Sequence QC

data/nextstrain/ndv/class-1/AB524405/genome_annotation.gff3

@@ -0,0 +1,12 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+##sequence-region AB524405.1 1 15198
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2560319
+AB524405.1	DDBJ	region	1	15198	.	+	.	ID=AB524405.1:1..15198;Dbxref=taxon:2560319;gbkey=Src;isolate=Goose/Alaska/415/91;mol_type=viral cRNA;note=lineage 6;old-name=Avian orthoavulavirus 1
+AB524405.1	DDBJ	CDS	122	1591	.	+	0	Name=N;gene=N;gbkey=CDS;protein_id=BAI66067.1;ID=cds-BAI66067.1;Dbxref=NCBI_GP:BAI66067.1;product=nucleocapsid protein
+AB524405.1	DDBJ	CDS	1887	3086	.	+	0	Name=P;gene=P;gbkey=CDS;protein_id=BAI66068.1;ID=cds-BAI66068.1;product=phosphoprotein;Dbxref=NCBI_GP:BAI66068.1
+AB524405.1	DDBJ	CDS	3302	4396	.	+	0	Name=M;gene=M;gbkey=CDS;protein_id=BAI66069.1;ID=cds-BAI66069.1;product=matrix protein;Dbxref=NCBI_GP:BAI66069.1
+AB524405.1	DDBJ	CDS	4556	6217	.	+	0	Name=F;gene=F;gbkey=CDS;protein_id=BAI66070.1;ID=cds-BAI66070.1;product=fusion protein;Dbxref=NCBI_GP:BAI66070.1
+AB524405.1	DDBJ	CDS	6424	8274	.	+	0	Name=HN;gene=HN;gbkey=CDS;protein_id=BAI66071.1;ID=cds-BAI66071.1;Dbxref=NCBI_GP:BAI66071.1;product=hemagglutinin-neuraminidase protein
+AB524405.1	DDBJ	CDS	8393	15007	.	+	0	Name=L;gene=L;gbkey=CDS;protein_id=BAI66072.1;ID=cds-BAI66072.1;Dbxref=NCBI_GP:BAI66072.1;product=large polymerase protein

data/nextstrain/ndv/class-1/AB524405/pathogen.json

@@ -0,0 +1,97 @@
+{
+  "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json",
+  "schemaVersion": "3.0.0",
+  "alignmentParams": {
+    "penaltyGapOpen": 12,
+    "penaltyGapOpenInFrame": 16,
+    "penaltyGapOpenOutOfFrame": 18,
+    "penaltyGapExtend": 1,
+    "gapAlignmentSide": "left",
+    "excessBandwidth": 50,
+    "terminalBandwidth": 50,
+    "minSeedCover": 0.1,
+    "kmerLength": 5,
+    "kmerDistance": 7,
+    "minMatchLength": 20,
+    "allowedMismatches": 10,
+    "windowSize": 30
+  },
+  "compatibility": {
+    "cli": "3.0.0-alpha.0",
+    "web": "3.0.0-alpha.0"
+  },
+  "defaultCds": "F",
+  "files": {
+    "examples": "sequences.fasta",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "pathogenJson": "pathogen.json",
+    "reference": "reference.fasta",
+    "treeJson": "tree.json",
+    "readme": "README.md",
+    "changelog": "CHANGELOG.md"
+  },
+  "qc": {
+    "privateMutations": {
+      "enabled": true,
+      "typical": 150,
+      "cutoff": 200,
+      "weightLabeledSubstitutions": 2,
+      "weightReversionSubstitutions": 1,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "missingData": {
+      "enabled": false,
+      "missingDataThreshold": 3000,
+      "scoreBias": 500
+    },
+    "snpClusters": {
+      "enabled": false,
+      "windowSize": 100,
+      "clusterCutOff": 10,
+      "scoreWeight": 50
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 10
+    },
+    "frameShifts": {
+      "enabled": true,
+      "scoreWeight": 50,
+      "ignoredFrameShifts": []
+    },
+    "stopCodons": {
+      "enabled": true,
+      "ignoredStopCodons": [
+        {
+          "cdsName": "HN",
+          "codon": 585
+        },
+        {
+          "cdsName": "HN",
+          "codon": 591
+        },
+        {
+          "cdsName": "HN",
+          "codon": 612
+        }
+      ],
+      "scoreWeight": 50
+    }
+  },
+  "shortcuts": [
+    "ndv-class-1"
+  ],
+  "attributes": {
+    "name": "Newcastle disease virus class 1",
+    "reference accession": "AB524405",
+    "reference name": "Goose/Alaska/415/91"
+  },
+  "cdsOrderPreference": [
+    "N",
+    "P",
+    "M",
+    "F",
+    "HN",
+    "L"
+  ]
+}