bdbv: first stab at bdbv dataset

data/nextstrain/collection.json

@@ -100,6 +100,7 @@
     "nextstrain/flu/h2n2/ha",
     "nextstrain/flu/h2n2/na",
     "nextstrain/flu/h2n2/mp",
-    "nextstrain/flu/h2n2/ns"
+    "nextstrain/flu/h2n2/ns",
+    "nextstrain/orthoebolavirus/bdbv"
   ]
 }

data/nextstrain/orthoebolavirus/bdbv/CHANGELOG.md

@@ -0,0 +1,2 @@
+## Unreleased
+

data/nextstrain/orthoebolavirus/bdbv/README.md

@@ -0,0 +1,11 @@
+# Nextclade dataset for Bundibugyo virus (Orthoebolavirus bundibugyoense)
+
+| Key                    | Value                                                                           |
+| ---------------------- | ------------------------------------------------------------------------------- |
+| authors                | [Richard Neher](https://neherlab.org) |
+| data source            | Genbank                                                                         |
+| nextclade dataset path | nextstrain/orthoebolavirus/bdbv                                                |
+| annotation             | [NC_014373.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_014373.1)                   |
+
+Bundibugyo virus [(Orthoebolavirus bundibugyoense)](https://ictv.global/report/chapter/filoviridae/filoviridae/orthoebolavirus).
+

data/nextstrain/orthoebolavirus/bdbv/genome_annotation.gff3

@@ -0,0 +1,15 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+##sequence-region NC_014373.1 1 18940
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=565995
+NC_014373.1	RefSeq	region	1	18940	.	+	.	ID=NC_014373.1:1..18940;Dbxref=taxon:565995;collection-date=Nov-2007;country=Uganda;gbkey=Src;genome=genomic;isolate=Bundibugyo virus/H.sapiens-tc/UGA/2007/Butalya-811250;isolation-source=blood;mol_type=viral cRNA;nat-host=Homo sapiens;old-name=Bundibugyo ebolavirus
+NC_014373.1	RefSeq	CDS	458	2677	.	+	0	Name=NP;gene=NP;gbkey=CDS;locus_tag=BDBVp1;product=nucleoprotein;protein_id=YP_003815432.1;ID=cds-YP_003815432.1;Note=encapsidation of genomic RNA;Dbxref=GenBank:YP_003815432.1,GeneID:9487269
+NC_014373.1	RefSeq	CDS	3108	4133	.	+	0	Name=VP35;gbkey=CDS;gene=VP35;locus_tag=BDBVp2;protein_id=YP_003815433.1;ID=cds-YP_003815433.1;product=polymerase complex protein;Note=putative type-1 IFN antagonist;Dbxref=GenBank:YP_003815433.1,GeneID:9487263
+NC_014373.1	RefSeq	CDS	4461	5441	.	+	0	Name=VP40;gbkey=CDS;gene=VP40;locus_tag=BDBVp3;product=matrix protein;protein_id=YP_003815434.1;ID=cds-YP_003815434.1;Dbxref=GenBank:YP_003815434.1,GeneID:9487264
+NC_014373.1	RefSeq	CDS	6021	6905	.	+	0	Name=GP;gene=GP;gbkey=CDS;locus_tag=BDBVp4;exception=RNA editing;protein_id=YP_003815435.1;ID=cds-YP_003815435.1;product=spike glycoprotein;Dbxref=GenBank:YP_003815435.1,GeneID:9487265;Note=GP1%2C2%3B structural glycoprotein%3B cleaved by furin into subunits GP1 and GP2 to yield a heterodimer linked by a disulfide bond
+NC_014373.1	RefSeq	CDS	6905	8050	.	+	0	Name=GP;gene=GP;gbkey=CDS;locus_tag=BDBVp4;exception=RNA editing;protein_id=YP_003815435.1;ID=cds-YP_003815435.1;product=spike glycoprotein;Dbxref=GenBank:YP_003815435.1,GeneID:9487265;Note=GP1%2C2%3B structural glycoprotein%3B cleaved by furin into subunits GP1 and GP2 to yield a heterodimer linked by a disulfide bond
+NC_014373.1	RefSeq	CDS	6021	7142	.	+	0	Name=GP_003;gene=GP;gbkey=CDS;locus_tag=BDBVp4;protein_id=YP_003815436.1;ID=cds-YP_003815436.1;product=small secreted glycoprotein;Dbxref=GenBank:YP_003815436.1,GeneID:9487265;Note=solulbe secreted glycoprotein%3B small non-structural secreted glycoprotein%3B sGP
+NC_014373.1	RefSeq	CDS	8496	9365	.	+	0	Name=VP30;gbkey=CDS;gene=VP30;locus_tag=BDBVp5;protein_id=YP_003815438.1;ID=cds-YP_003815438.1;product=minor nucleoprotein;Note=polymerase complex protein;Dbxref=GenBank:YP_003815438.1,GeneID:9487266
+NC_014373.1	RefSeq	CDS	10335	11090	.	+	0	Name=VP24;gbkey=CDS;gene=VP24;locus_tag=BDBVp6;protein_id=YP_003815439.1;ID=cds-YP_003815439.1;product=membrane-associated protein;Dbxref=GenBank:YP_003815439.1,GeneID:9487267
+NC_014373.1	RefSeq	CDS	11567	18199	.	+	0	Name=L;gene=L;gbkey=CDS;locus_tag=BDBVp7;protein_id=YP_003815440.1;ID=cds-YP_003815440.1;product=RNA-dependent RNA polymerase;Dbxref=GenBank:YP_003815440.1,GeneID:9487268;Note=synthesis of viral RNAs%3B transcriptional RNA editing

data/nextstrain/orthoebolavirus/bdbv/pathogen.json

@@ -0,0 +1,78 @@
+{
+  "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json",
+  "alignmentParams": {
+    "excessBandwidth": 100,
+    "terminalBandwidth": 300,
+    "allowedMismatches": 10,
+    "windowSize": 40,
+    "minSeedCover": 0.03,
+    "gapAlignmentSide": "left"
+  },
+  "attributes": {
+    "name": "Bundibugyo ebolavirus",
+    "reference accession": "NC_014373.1",
+    "reference name": "UGA/2007/Butalya-811250",
+    "experimental": true
+  },
+  "compatibility": {
+    "cli": "3.0.0-alpha.0",
+    "web": "3.0.0-alpha.0"
+  },
+  "files": {
+    "treeJson": "tree.json",
+    "changelog": "CHANGELOG.md",
+    "examples": "examples.fasta",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "pathogenJson": "pathogen.json",
+    "readme": "README.md",
+    "reference": "reference.fasta"
+  },
+  "defaultCds": "GP",
+  "qc": {
+    "frameShifts": {
+      "enabled": true,
+      "ignoredFrameShifts": [],
+      "scoreWeight": 20
+    },
+    "missingData": {
+      "enabled": true,
+      "missingDataThreshold": 3000,
+      "scoreBias": 500
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 40
+    },
+    "privateMutations": {
+      "cutoff": 300,
+      "enabled": true,
+      "typical": 50,
+      "weightLabeledSubstitutions": 6,
+      "weightReversionSubstitutions": 6,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "snpClusters": {
+      "clusterCutOff": 10,
+      "enabled": false,
+      "scoreWeight": 10,
+      "windowSize": 100
+    },
+    "stopCodons": {
+      "enabled": true,
+      "ignoredStopCodons": [],
+      "scoreWeight": 20
+    }
+  },
+  "schemaVersion": "3.0.0",
+  "shortcuts": [
+    "nextstrain/ebola/bebov"
+  ],
+  "version": {
+    "updatedAt": "2026-04-14T11:55:23Z",
+    "tag": "2026-04-14--11-55-23Z",
+    "compatibility": {
+      "cli": "3.0.0-alpha.0",
+      "web": "3.0.0-alpha.0"
+    }
+  }
+}