West Nile Virus overview

data/nextstrain/collection.json

@@ -51,6 +51,11 @@
     "nextstrain/flu/h3n2/pa",
     "nextstrain/flu/h1n1pdm/pb2",
     "nextstrain/flu/h1n1pdm/pb1",
-    "nextstrain/flu/h3n2/pb2"
+    "nextstrain/flu/h3n2/pb2",
+    "nextstrain/ebola/zaire",
+    "nextstrain/ebola/sudan",
+    "nextstrain/wnv/lineage-2",
+    "nextstrain/wnv/lineage-1",
+    "nextstrain/wnv/all-lineages"
   ]
 }

data/nextstrain/wnv/all-lineages/CHANGELOG.md

@@ -0,0 +1,3 @@
+## Unreleased
+
+Initial release of this dataset.

data/nextstrain/wnv/all-lineages/README.md

@@ -0,0 +1,24 @@
+# Nextclade dataset for West Nile virus
+
+| Key                    | Value                                                                                                                    |
+| ---------------------- | ------------------------------------------------------------------------------------------------------------------------ |
+| authors                | [Cornelius Roemer](https://neherlab.org), [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org)    |
+| data source            | Genbank                                                                                                                  |
+| workflow               | [github.com/neherlab/nextclade_data_workflows/west-nile](https://github.com/neherlab/nextclade_data_workflows/west-nile) |
+| nextclade dataset path | nextstrain/west-nile                                                                                                     |
+| annotation             | [NC_009942.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_009942)                                                            |
+| clade definitions      | from genomedetective.com: <https://www.genomedetective.com/app/typingtool/wnv/introduction>                              |
+
+## Scope of this dataset
+
+This dataset is intended to be used to classify West Nile virus sequences into major lineages.
+
+## Reference sequence and reference tree
+
+The reference used in this dataset is the lineage 1A NCBI refseq `NC_009942.1` (Isolate `NY99`).
+
+The reference tree consists of around 100 sequences with representatives from all 8 lineages.
+
+## Further reading
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/nextstrain/wnv/all-lineages/genome_annotation.gff3

@@ -0,0 +1,18 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+##sequence-region NC_009942.1 1 11029
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=11082
+NC_009942.1	RefSeq	region	1	11029	.	+	.	ID=NC_009942.1:1..11029;Dbxref=taxon:11082;country=USA;gb-acronym=WNV;gbkey=Src;genome=genomic;isolate=385-99;mol_type=genomic RNA;note=lineage 1%3B Vero cell passage 2 after isolation;strain=NY99
+NC_009942.1	RefSeq	gene	97	10395	.	+	.	gene=POLY;ID=gene-WNVNY99_gp1;gbkey=Prot;product=anchored capsid protein ancC;protein_id=YP_005097850.1
+NC_009942.1	RefSeq	CDS	97	465	.	+	.	gene=capsid;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=anchored capsid protein ancC;protein_id=YP_005097850.1
+NC_009942.1	RefSeq	CDS	466	966	.	+	.	gene=prM;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=protein pr;protein_id=YP_009164953.1
+NC_009942.1	RefSeq	CDS	967	2469	.	+	.	gene=env;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=envelope protein E;protein_id=YP_001527880.1
+NC_009942.1	RefSeq	CDS	2470	3525	.	+	.	gene=NS1;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS1;protein_id=YP_001527881.1
+NC_009942.1	RefSeq	CDS	3526	4218	.	+	.	gene=NS2A;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS2A;protein_id=YP_001527882.1
+NC_009942.1	RefSeq	CDS	4219	4611	.	+	.	gene=NS2B;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS2B;protein_id=YP_001527883.1
+NC_009942.1	RefSeq	CDS	4612	6468	.	+	.	gene=NS3;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS3;protein_id=YP_001527884.1
+NC_009942.1	RefSeq	CDS	6469	6846	.	+	.	gene=NS4A;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS4A;protein_id=YP_001527885.1
+NC_009942.1	RefSeq	CDS	6847	6915	.	+	.	gene=2K;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=protein 2K;protein_id=YP_001527885.1
+NC_009942.1	RefSeq	CDS	6916	7680	.	+	.	gene=NS4B;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS4B;protein_id=YP_001527886.1
+NC_009942.1	RefSeq	CDS	7681	10395	.	+	.	gene=NS5;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=RNA-dependent RNA polymerase NS5;protein_id=YP_001527887.1

data/nextstrain/wnv/all-lineages/pathogen.json

@@ -0,0 +1,72 @@
+{
+  "alignmentParams": {
+    "excessBandwidth": 40,
+    "terminalBandwidth": 200,
+    "allowedMismatches": 5,
+    "windowSize": 30,
+    "minSeedCover": 0.01,
+    "gapAlignmentSide": "left"
+  },
+  "attributes": {
+    "name": "West Nile Virus",
+    "reference accession": "NC_009942.1",
+  "reference name": "Strain NY99 (lineage 1A)"
+  },
+  "compatibility": {
+    "cli": "3.0.0-alpha.0",
+    "web": "3.0.0-alpha.0"
+  },
+  "deprecated": false,
+  "enabled": true,
+  "experimental": false,
+  "files": {
+    "changelog": "CHANGELOG.md",
+    "examples": "examples.fasta",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "pathogenJson": "pathogen.json",
+    "readme": "README.md",
+    "reference": "reference.fasta",
+    "treeJson": "tree.json"
+  },
+  "official": true,
+  "qc": {
+    "frameShifts": {
+      "enabled": true,
+      "scoreWeight": 20
+    },
+    "missingData": {
+      "enabled": true,
+      "missingDataThreshold": 20000,
+      "scoreBias": 1000
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 40
+    },
+    "privateMutations": {
+      "cutoff": 200,
+      "enabled": true,
+      "typical": 50,
+      "weightLabeledSubstitutions": 1,
+      "weightReversionSubstitutions": 2,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "snpClusters": {
+      "clusterCutOff": 5,
+      "enabled": false,
+      "scoreWeight": 20,
+      "windowSize": 100
+    },
+    "stopCodons": {
+      "enabled": true,
+      "scoreWeight": 40
+    }
+  },
+  "schemaVersion": "3.0.0",
+  "shortcuts": [
+    "wnv", "west-nile", "west-nile-virus"
+  ],
+  "version": {
+    "tag": "unreleased"
+  }
+}

data/nextstrain/wnv/all-lineages/reference.fasta

@@ -0,0 +1,159 @@
+>NC_009942.1 West Nile virus lineage 1, complete genome
+AGTAGTTCGCCTGTGTGAGCTGACAAACTTAGTAGTGTTTGTGAGGATTAACAACAATTAACACAGTGCG
+AGCTGTTTCTTAGCACGAAGATCTCGATGTCTAAGAAACCAGGAGGGCCCGGCAAGAGCCGGGCTGTCAA
+TATGCTAAAACGCGGAATGCCCCGCGTGTTGTCCTTGATTGGACTGAAGAGGGCTATGTTGAGCCTGATC
+GACGGCAAGGGGCCAATACGATTTGTGTTGGCTCTCTTGGCGTTCTTCAGGTTCACAGCAATTGCTCCGA
+CCCGAGCAGTGCTGGATCGATGGAGAGGTGTGAACAAACAAACAGCGATGAAACACCTTCTGAGTTTTAA
+GAAGGAACTAGGGACCTTGACCAGTGCTATCAATCGGCGGAGCTCAAAACAAAAGAAAAGAGGAGGAAAG
+ACCGGAATTGCAGTCATGATTGGCCTGATCGCCAGCGTAGGAGCAGTTACCCTCTCTAACTTCCAAGGGA
+AGGTGATGATGACGGTAAATGCTACTGACGTCACAGATGTCATCACGATTCCAACAGCTGCTGGAAAGAA
+CCTATGCATTGTCAGAGCAATGGATGTGGGATACATGTGCGATGATACTATCACTTATGAATGCCCAGTA
+CTGTCGGCTGGTAATGATCCAGAAGACATCGACTGTTGGTGCACAAAGTCAGCAGTCTACGTCAGGTATG
+GAAGATGCACCAAGACACGCCACTCAAGACGCAGTCGGAGGTCACTGACAGTGCAGACACACGGAGAAAG
+CACTCTAGCGAACAAGAAGGGGGCTTGGATGGACAGCACCAAGGCCACAAGGTATTTGGTAAAAACAGAA
+TCATGGATCTTGAGGAACCCTGGATATGCCCTGGTGGCAGCCGTCATTGGTTGGATGCTTGGGAGCAACA
+CCATGCAGAGAGTTGTGTTTGTCGTGCTATTGCTTTTGGTGGCCCCAGCTTACAGCTTCAACTGCCTTGG
+AATGAGCAACAGAGACTTCTTGGAAGGAGTGTCTGGAGCAACATGGGTGGATTTGGTTCTCGAAGGCGAC
+AGCTGCGTGACTATCATGTCTAAGGACAAGCCTACCATCGATGTGAAGATGATGAATATGGAGGCGGCCA
+ACCTGGCAGAGGTCCGCAGTTATTGCTATTTGGCTACCGTCAGCGATCTCTCCACCAAAGCTGCGTGCCC
+GACCATGGGAGAAGCTCACAATGACAAACGTGCTGACCCAGCTTTTGTGTGCAGACAAGGAGTGGTGGAC
+AGGGGCTGGGGCAACGGCTGCGGACTATTTGGCAAAGGAAGCATTGACACATGCGCCAAATTTGCCTGCT
+CTACCAAGGCAATAGGAAGAACCATCTTGAAAGAGAATATCAAGTACGAAGTGGCCATTTTTGTCCATGG
+ACCAACTACTGTGGAGTCGCACGGAAACTACTCCACACAGGTTGGAGCCACTCAGGCAGGGAGACTCAGC
+ATCACTCCTGCGGCGCCTTCATACACACTAAAGCTTGGAGAATATGGAGAGGTGACAGTGGACTGTGAAC
+CACGGTCAGGGATTGACACCAATGCATACTACGTGATGACTGTTGGAACAAAGACGTTCTTGGTCCATCG
+TGAGTGGTTCATGGACCTCAACCTCCCTTGGAGCAGTGCTGGAAGTACTGTGTGGAGGAACAGAGAGACG
+TTAATGGAGTTTGAGGAACCACACGCCACGAAGCAGTCTGTGATAGCATTGGGCTCACAAGAGGGAGCTC
+TGCATCAAGCTTTGGCTGGAGCCATTCCTGTGGAATTTTCAAGCAACACTGTCAAGTTGACGTCGGGTCA
+TTTGAAGTGTAGAGTGAAGATGGAAAAATTGCAGTTGAAGGGAACAACCTATGGCGTCTGTTCAAAGGCT
+TTCAAGTTTCTTGGGACTCCCGCAGACACAGGTCACGGCACTGTGGTGTTGGAATTGCAGTACACTGGCA
+CGGATGGACCTTGCAAAGTTCCTATCTCGTCAGTGGCTTCATTGAACGACCTAACGCCAGTGGGCAGATT
+GGTCACTGTCAACCCTTTTGTTTCAGTGGCCACGGCCAACGCTAAGGTCCTGATTGAATTGGAACCACCC
+TTTGGAGACTCATACATAGTGGTGGGCAGAGGAGAACAACAGATCAATCACCATTGGCACAAGTCTGGAA
+GCAGCATTGGCAAAGCCTTTACAACCACCCTCAAAGGAGCGCAGAGACTAGCCGCTCTAGGAGACACAGC
+TTGGGACTTTGGATCAGTTGGAGGGGTGTTCACCTCAGTTGGGAAGGCTGTCCATCAAGTGTTCGGAGGA
+GCATTCCGCTCACTGTTCGGAGGCATGTCCTGGATAACGCAAGGATTGCTGGGGGCTCTCCTGTTGTGGA
+TGGGCATCAATGCTCGTGATAGGTCCATAGCTCTCACGTTTCTCGCAGTTGGAGGAGTTCTGCTCTTCCT
+CTCCGTGAACGTGCACGCTGACACTGGGTGTGCCATAGACATCAGCCGGCAAGAGCTGAGATGTGGAAGT
+GGAGTGTTCATACACAATGATGTGGAGGCTTGGATGGACCGGTACAAGTATTACCCTGAAACGCCACAAG
+GCCTAGCCAAGATCATTCAGAAAGCTCATAAGGAAGGAGTGTGCGGTCTACGATCAGTTTCCAGACTGGA
+GCATCAAATGTGGGAAGCAGTGAAGGACGAGCTGAACACTCTTTTGAAGGAGAATGGTGTGGACCTTAGT
+GTCGTGGTTGAGAAACAGGAGGGAATGTACAAGTCAGCACCTAAACGCCTCACCGCCACCACGGAAAAAT
+TGGAAATTGGCTGGAAGGCCTGGGGAAAGAGTATTTTATTTGCACCAGAACTCGCCAACAACACCTTTGT
+GGTTGATGGTCCGGAGACCAAGGAATGTCCGACTCAGAATCGCGCTTGGAATAGCTTAGAAGTGGAGGAT
+TTTGGATTTGGTCTCACCAGCACTCGGATGTTCCTGAAGGTCAGAGAGAGCAACACAACTGAATGTGACT
+CGAAGATCATTGGAACGGCTGTCAAGAACAACTTGGCGATCCACAGTGACCTGTCCTATTGGATTGAAAG
+CAGGCTCAATGATACGTGGAAGCTTGAAAGGGCAGTTCTGGGTGAAGTCAAATCATGTACGTGGCCTGAG
+ACGCATACCTTGTGGGGCGATGGAATCCTTGAGAGTGACTTGATAATACCAGTCACACTGGCGGGACCAC
+GAAGCAATCACAATCGGAGACCTGGGTACAAGACACAAAACCAGGGCCCATGGGACGAAGGCCGGGTAGA
+GATTGACTTCGATTACTGCCCAGGAACTACGGTCACCCTGAGTGAGAGCTGCGGACACCGTGGACCTGCC
+ACTCGCACCACCACAGAGAGCGGAAAGTTGATAACAGATTGGTGCTGCAGGAGCTGCACCTTACCACCAC
+TGCGCTACCAAACTGACAGCGGCTGTTGGTATGGTATGGAGATCAGACCACAGAGACATGATGAAAAGAC
+CCTCGTGCAGTCACAAGTGAATGCTTATAATGCTGATATGATTGACCCTTTTCAGTTGGGCCTTCTGGTC
+GTGTTCTTGGCCACCCAGGAGGTCCTTCGCAAGAGGTGGACAGCCAAGATCAGCATGCCAGCTATACTGA
+TTGCTCTGCTAGTCCTGGTGTTTGGGGGCATTACTTACACTGATGTGTTACGCTATGTCATCTTGGTGGG
+GGCAGCTTTCGCAGAATCTAATTCGGGAGGAGACGTGGTACACTTGGCGCTCATGGCGACCTTCAAGATA
+CAACCAGTGTTTATGGTGGCATCGTTTCTCAAAGCGAGATGGACCAACCAGGAGAACATTTTGTTGATGT
+TGGCGGCTGTTTTCTTTCAAATGGCTTATCACGATGCCCGCCAAATTCTGCTCTGGGAGATCCCTGATGT
+GTTGAATTCACTGGCGGTAGCTTGGATGATACTGAGAGCCATAACATTCACAACGACATCAAACGTGGTT
+GTTCCGCTGCTAGCCCTGCTAACACCCGGGCTGAGATGCTTGAATCTGGATGTGTACAGGATACTGCTGT
+TGATGGTCGGAATAGGCAGCTTGATCAGGGAGAAGAGGAGTGCAGCCGCAAAAAAGAAAGGAGCAAGTCT
+GCTATGCTTGGCTCTAGCCTCAACAGGACTTTTCAACCCCATGATCCTTGCTGCTGGACTGATTGCATGT
+GATCCCAACCGTAAACGCGGATGGCCCGCAACTGAAGTGATGACAGCTGTCGGCCTAATGTTTGCCATCG
+TCGGAGGGCTGGCAGAGCTTGACATTGACTCCATGGCCATTCCAATGACTATCGCGGGGCTCATGTTTGC
+TGCTTTCGTGATTTCTGGGAAATCAACAGATATGTGGATTGAGAGAACGGCGGACATTTCCTGGGAAAGT
+GATGCAGAAATTACAGGCTCGAGCGAAAGAGTTGATGTGCGGCTTGATGATGATGGAAACTTCCAGCTCA
+TGAATGATCCAGGAGCACCTTGGAAGATATGGATGCTCAGAATGGTCTGTCTCGCGATTAGTGCGTACAC
+CCCCTGGGCAATCTTGCCCTCAGTAGTTGGATTTTGGATAACTCTCCAATACACAAAGAGAGGAGGCGTG
+TTGTGGGACACTCCCTCACCAAAGGAGTACAAAAAGGGGGACACGACCACCGGCGTCTACAGGATCATGA
+CTCGTGGGCTGCTCGGCAGTTATCAAGCAGGAGCGGGCGTGATGGTTGAAGGTGTTTTCCACACCCTTTG
+GCATACAACAAAAGGAGCCGCTTTGATGAGCGGAGAGGGCCGCCTGGACCCATACTGGGGCAGTGTCAAG
+GAGGATCGACTTTGTTACGGAGGACCCTGGAAATTGCAGCACAAGTGGAACGGGCAGGATGAGGTGCAGA
+TGATTGTGGTGGAACCTGGCAAGAACGTTAAGAACGTCCAGACGAAACCAGGGGTGTTCAAAACACCTGA
+AGGAGAAATCGGGGCCGTGACTTTGGACTTCCCCACTGGAACATCAGGCTCACCAATAGTGGACAAAAAC
+GGTGATGTGATTGGGCTTTATGGCAATGGAGTCATAATGCCCAACGGCTCATACATAAGCGCGATAGTGC
+AGGGTGAAAGGATGGATGAGCCAATCCCAGCCGGATTCGAACCTGAGATGCTGAGGAAAAAACAGATCAC
+TGTACTGGATCTCCATCCCGGCGCCGGTAAAACAAGGAGGATTCTGCCACAGATCATCAAAGAGGCCATA
+AACAGAAGACTGAGAACAGCCGTGCTAGCGCCAACCAGGGTTGTGGCTGCTGAGATGGCTGAAGCACTGA
+GAGGACTGCCCATCCGGTACCAGACATCCGCAGTGCCCAGAGAACATAATGGAAATGAGATTGTTGATGT
+CATGTGTCATGCTACCCTCACCCACAGGCTGATGTCTCCTCACAGGGTGCCGAACTACAACCTGTTCGTG
+ATGGATGAGGCTCATTTCACCGACCCAGCTAGCATTGCAGCAAGAGGTTACATTTCCACAAAGGTCGAGC
+TAGGGGAGGCGGCGGCAATATTCATGACAGCCACCCCACCAGGCACTTCAGATCCATTCCCAGAGTCCAA
+TTCACCAATTTCCGACTTACAGACTGAGATCCCGGATCGAGCTTGGAACTCTGGATACGAATGGATCACA
+GAATACACCGGGAAGACGGTTTGGTTTGTGCCTAGTGTCAAGATGGGGAATGAGATTGCCCTTTGCCTAC
+AACGTGCTGGAAAGAAAGTAGTCCAATTGAACAGAAAGTCGTACGAGACGGAGTACCCAAAATGTAAGAA
+CGATGATTGGGACTTTGTTATCACAACAGACATATCTGAAATGGGGGCTAACTTCAAGGCGAGCAGGGTG
+ATTGACAGCCGGAAGAGTGTGAAACCAACCATCATAACAGAAGGAGAAGGGAGAGTGATCCTGGGAGAAC
+CATCTGCAGTGACAGCAGCTAGTGCCGCCCAGAGACGTGGACGTATCGGTAGAAATCCGTCGCAAGTTGG
+TGATGAGTACTGTTATGGGGGGCACACGAATGAAGACGACTCGAACTTCGCCCATTGGACTGAGGCACGA
+ATCATGCTGGACAACATCAACATGCCAAACGGACTGATCGCTCAATTCTACCAACCAGAGCGTGAGAAGG
+TATATACCATGGATGGGGAATACCGGCTCAGAGGAGAAGAGAGAAAAAACTTTCTGGAACTGTTGAGGAC
+TGCAGATCTGCCAGTTTGGCTGGCTTACAAGGTTGCAGCGGCTGGAGTGTCATACCACGACCGGAGGTGG
+TGCTTTGATGGTCCTAGGACAAACACAATTTTAGAAGACAACAACGAAGTGGAAGTCATCACGAAGCTTG
+GTGAAAGGAAGATTCTGAGGCCGCGCTGGATTGATGCCAGGGTGTACTCGGATCACCAGGCACTAAAGGC
+GTTCAAGGACTTCGCCTCGGGAAAACGTTCTCAGATAGGGCTCATTGAGGTTCTGGGAAAGATGCCTGAG
+CACTTCATGGGGAAGACATGGGAAGCACTTGACACCATGTACGTTGTGGCCACTGCAGAGAAAGGAGGAA
+GAGCTCACAGAATGGCCCTGGAGGAACTGCCAGATGCTCTTCAGACAATTGCCTTGATTGCCTTATTGAG
+TGTGATGACCATGGGAGTATTCTTCCTCCTCATGCAGCGGAAGGGCATTGGAAAGATAGGTTTGGGAGGC
+GCTGTCTTGGGAGTCGCGACCTTTTTCTGTTGGATGGCTGAAGTTCCAGGAACGAAGATCGCCGGAATGT
+TGCTGCTCTCCCTTCTCTTGATGATTGTGCTAATTCCTGAGCCAGAGAAGCAACGTTCGCAGACAGACAA
+CCAGCTAGCCGTGTTCCTGATTTGTGTCATGACCCTTGTGAGCGCAGTGGCAGCCAACGAGATGGGTTGG
+CTAGATAAGACCAAGAGTGACATAAGCAGTTTGTTTGGGCAAAGAATTGAGGTCAAGGAGAATTTCAGCA
+TGGGAGAGTTTCTTCTGGACTTGAGGCCGGCAACAGCCTGGTCACTGTACGCTGTGACAACAGCGGTCCT
+CACTCCACTGCTAAAGCATTTGATCACGTCAGATTACATCAACACCTCATTGACCTCAATAAACGTTCAG
+GCAAGTGCACTATTCACACTCGCGCGAGGCTTCCCCTTCGTCGATGTTGGAGTGTCGGCTCTCCTGCTAG
+CAGCCGGATGCTGGGGACAAGTCACCCTCACCGTTACGGTAACAGCGGCAACACTCCTTTTTTGCCACTA
+TGCCTACATGGTTCCCGGTTGGCAAGCTGAGGCAATGCGCTCAGCCCAGCGGCGGACAGCGGCCGGAATC
+ATGAAGAACGCTGTAGTGGATGGCATCGTGGCCACGGACGTCCCAGAATTAGAGCGCACCACACCCATCA
+TGCAGAAGAAAGTTGGACAGATCATGCTGATCTTGGTGTCTCTAGCTGCAGTAGTAGTGAACCCGTCTGT
+GAAGACAGTACGAGAAGCCGGAATTTTGATCACGGCCGCAGCGGTGACGCTTTGGGAGAATGGAGCAAGC
+TCTGTTTGGAACGCAACAACTGCCATCGGACTCTGCCACATCATGCGTGGGGGTTGGTTGTCATGTCTAT
+CCATAACATGGACACTCATAAAGAACATGGAAAAACCAGGACTAAAAAGAGGTGGGGCAAAAGGACGCAC
+CTTGGGAGAGGTTTGGAAAGAAAGACTCAACCAGATGACAAAAGAAGAGTTCACTAGGTACCGCAAAGAG
+GCCATCATCGAAGTCGATCGCTCAGCGGCAAAACACGCCAGGAAAGAAGGCAATGTCACTGGAGGGCATC
+CAGTCTCTAGGGGCACAGCAAAACTGAGATGGCTGGTCGAACGGAGGTTTCTCGAACCGGTCGGAAAAGT
+GATTGACCTTGGATGTGGAAGAGGCGGTTGGTGTTACTATATGGCAACCCAAAAAAGAGTCCAAGAAGTC
+AGAGGGTACACAAAGGGCGGTCCCGGACATGAAGAGCCCCAACTAGTGCAAAGTTATGGATGGAACATTG
+TCACCATGAAGAGTGGAGTGGATGTGTTCTACAGACCTTCTGAGTGTTGTGACACCCTCCTTTGTGACAT
+CGGAGAGTCCTCGTCAAGTGCTGAGGTTGAAGAGCATAGGACGATTCGGGTCCTTGAAATGGTTGAGGAC
+TGGCTGCACCGAGGGCCAAGGGAATTTTGCGTGAAGGTGCTCTGTCCCTACATGCCGAAAGTCATAGAGA
+AGATGGAGCTGCTCCAACGCCGGTATGGGGGGGGACTGGTCAGAAACCCACTCTCACGGAATTCCACGCA
+CGAGATGTATTGGGTGAGTCGAGCTTCAGGCAATGTGGTACATTCAGTGAATATGACCAGCCAGGTGCTC
+CTAGGAAGAATGGAAAAAAGGACCTGGAAGGGACCCCAATACGAGGAAGATGTAAACTTGGGAAGTGGAA
+CCAGGGCGGTGGGAAAACCCCTGCTCAACTCAGACACCAGTAAAATCAAGAACAGGATTGAACGACTCAG
+GCGTGAGTACAGTTCGACGTGGCACCACGATGAGAACCACCCATATAGAACCTGGAACTATCACGGCAGT
+TATGATGTGAAGCCCACAGGCTCCGCCAGTTCGCTGGTCAATGGAGTGGTCAGGCTCCTCTCAAAACCAT
+GGGACACCATCACGAATGTTACCACCATGGCCATGACTGACACTACTCCCTTCGGGCAGCAGCGAGTGTT
+CAAAGAGAAGGTGGACACGAAAGCTCCTGAACCGCCAGAAGGAGTGAAGTACGTGCTCAACGAGACCACC
+AACTGGTTGTGGGCGTTTTTGGCCAGAGAAAAACGTCCCAGAATGTGCTCTCGAGAGGAATTCATAAGAA
+AGGTCAACAGCAATGCAGCTTTGGGTGCCATGTTTGAAGAGCAGAATCAATGGAGGAGCGCCAGAGAAGC
+AGTTGAAGATCCAAAATTTTGGGAGATGGTGGATGAGGAGCGCGAGGCACATCTGCGGGGGGAATGTCAC
+ACTTGCATTTACAACATGATGGGAAAGAGAGAGAAAAAACCCGGAGAGTTCGGAAAGGCCAAGGGAAGCA
+GAGCCATTTGGTTCATGTGGCTCGGAGCTCGCTTTCTGGAGTTCGAGGCTCTGGGTTTTCTCAATGAAGA
+CCACTGGCTTGGAAGAAAGAACTCAGGAGGAGGTGTCGAGGGCTTGGGCCTCCAAAAACTGGGTTACATC
+CTGCGTGAAGTTGGCACCCGGCCTGGGGGCAAGATCTATGCTGATGACACAGCTGGCTGGGACACCCGCA
+TCACGAGAGCTGACTTGGAAAATGAAGCTAAGGTGCTTGAGCTGCTTGATGGGGAACATCGGCGTCTTGC
+CAGGGCCATCATTGAGCTCACCTATCGTCACAAAGTTGTGAAAGTGATGCGCCCGGCTGCTGATGGAAGA
+ACCGTCATGGATGTTATCTCCAGAGAAGATCAGAGGGGGAGTGGACAAGTTGTCACCTACGCCCTAAACA
+CTTTCACCAACCTGGCCGTCCAGCTGGTGAGGATGATGGAAGGGGAAGGAGTGATTGGCCCAGATGATGT
+GGAGAAACTCACAAAAGGGAAAGGACCCAAAGTCAGGACCTGGCTGTTTGAGAATGGGGAAGAAAGACTC
+AGCCGCATGGCTGTCAGTGGAGATGACTGTGTGGTAAAGCCCCTGGACGATCGCTTTGCCACCTCGCTCC
+ACTTCCTCAATGCTATGTCAAAGGTTCGCAAAGACATCCAAGAGTGGAAACCGTCAACTGGATGGTATGA
+TTGGCAGCAGGTTCCATTTTGCTCAAACCATTTCACTGAATTGATCATGAAAGATGGAAGAACACTGGTG
+GTTCCATGCCGAGGACAGGATGAATTGGTAGGCAGAGCTCGCATATCTCCAGGGGCCGGATGGAACGTCC
+GCGACACTGCTTGTCTGGCTAAGTCTTATGCCCAGATGTGGCTGCTTCTGTACTTCCACAGAAGAGACCT
+GCGGCTCATGGCCAACGCCATTTGCTCCGCTGTCCCTGTGAATTGGGTCCCTACCGGAAGAACCACGTGG
+TCCATCCATGCAGGAGGAGAGTGGATGACAACAGAGGACATGTTGGAGGTCTGGAACCGTGTTTGGATAG
+AGGAGAATGAATGGATGGAAGACAAAACCCCAGTGGAGAAATGGAGTGACGTCCCATATTCAGGAAAACG
+AGAGGACATCTGGTGTGGCAGCCTGATTGGCACAAGAGCCCGAGCCACGTGGGCAGAAAACATCCAGGTG
+GCTATCAACCAAGTCAGAGCAATCATCGGAGATGAGAAGTATGTGGACTACATGAGTTCACTAAAGAGAT
+ATGAAGACACAACTTTGGTTGAGGACACAGTACTGTAGATATTTAATCAATTGTAAATAGACAATATAAG
+TATGCATAAAAGTGTAGTTTTATAGTAGTATTTAGTGGTGTTAGTGTAAATAGTTAAGAAAATTTTGAGG
+AGAAAGTCAGGCCGGGAAGTTCCCGCCACCGGAAGTTGAGTAGACGGTGCTGCCTGCGACTCAACCCCAG
+GAGGACTGGGTGAACAAAGCCGCGAAGTGATCCATGTAAGCCCTCAGAACCGTCTCGGAAGGAGGACCCC
+ACATGTTGTAACTTCAAAGCCCAATGTCAGACCACGCTACGGCGTGCTACTCTGCGGAGAGTGCAGTCTG
+CGATAGTGCCCCAGGAGGACTGGGTTAACAAAGGCAAACCAACGCCCCACGCGGCCCTAGCCCCGGTAAT
+GGTGTTAACCAGGGCGAAAGGACTAGAGGTTAGAGGAGACCCCGCGGTTTAAAGTGCACGGCCCAGCCTG
+GCTGAAGCTGTAGGTCAGGGGAAGGACTAGAGGTTAGTGGAGACCCCGTGCCACAAAACACCACAACAAA
+ACAGCATATTGACACCTGGGATAGACTAGGAGATCTTCTGCTCTGCACAACCAGCCACACGGCACAGTGC
+GCCGACAATGGTGGCTGGTGGTGCGAGAACACAGGATCT

data/nextstrain/wnv/lineage-1/CHANGELOG.md

@@ -0,0 +1,3 @@
+## Unreleased
+
+Initial release of this dataset.

data/nextstrain/wnv/lineage-1/README.md

@@ -0,0 +1,9 @@
+# Nextclade dataset for "Sudan Ebolavirus"
+
+| Key                    | Value                                                                           |
+| ---------------------- | ------------------------------------------------------------------------------- |
+| authors                | [Cornelius Roemer](https://neherlab.org), [Richard Neher](https://neherlab.org) |
+| data source            | Genbank                                                                         |
+| nextclade dataset path | nextstrain/ebola/sudan                                                          |
+| annotation             | [NC_006432.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_006432)                   |
+| related datasets       | Zaire Ebola virus: `nextstrain/ebola/zaire`                                     |