andv: initial addition

data/nextstrain/collection.json

@@ -97,6 +97,9 @@
     "nextstrain/flu/h2n2/na",
     "nextstrain/flu/h2n2/mp",
     "nextstrain/flu/h2n2/ns",
-    "nextstrain/wnv/all-lineages"
+    "nextstrain/wnv/all-lineages",
+    "nextstrain/orthohantavirus/andv/l",
+    "nextstrain/orthohantavirus/andv/m",
+    "nextstrain/orthohantavirus/andv/s"
   ]
 }

data/nextstrain/orthohantavirus/andv/l/CHANGELOG.md

@@ -0,0 +1,3 @@
+## Unreleased
+
+ - initial release

data/nextstrain/orthohantavirus/andv/l/README.md

@@ -0,0 +1,15 @@
+# Andesvirus segment L dataset
+
+| Key  | Value  |
+| :-- | :-- |
+| name  | Andes virus segment L Tree |
+| authors | [Nextstrain](https://nextstrain.org) |
+| reference | NC_003468 |
+| workflow  | https://github.com/nextstrain/andv/tree/main/nextclade  |
+| path  | `nextstrain/orthohantavirus/andv/l` |
+
+
+
+## What are Nextclade datasets
+
+Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/nextstrain/orthohantavirus/andv/l/genome_annotation.gff3

@@ -0,0 +1,7 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+##sequence-region NC_003468.2 1 6562
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1980456
+NC_003468.2	RefSeq	region	1	6562	.	+	.	ID=NC_003468.2:1..6562;Dbxref=taxon:1980456;Name=L;gbkey=Src;genome=genomic;mol_type=genomic RNA;old-name=Andes virus;segment=L;strain=Chile-9717869
+NC_003468.2	RefSeq	CDS	36	6497	.	+	0	Name=RdRp;gbkey=CDS;locus_tag=ANDVsLgp1;protein_id=NP_604473.1;product=RNA polymerase;ID=cds-NP_604473.1;Dbxref=GenBank:NP_604473.1,GeneID:991234

data/nextstrain/orthohantavirus/andv/l/pathogen.json

@@ -0,0 +1,63 @@
+{
+  "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json",
+  "files": {
+    "reference": "reference.fasta",
+    "pathogenJson": "pathogen.json",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "treeJson": "tree.json",
+    "examples": "sequences.fasta",
+    "readme": "README.md",
+    "changelog": "CHANGELOG.md"
+  },
+  "schemaVersion": "3.0.0",
+  "defaultCds": "RdRp",
+  "attributes": {
+    "name": "Andesvirus (segment L)",
+    "reference name": "Chile-9717869",
+    "reference accession": "NC_003468"
+  },
+  "experimental": true,
+  "alignmentParams": {
+    "penaltyGapExtend": 1,
+    "penaltyGapOpen": 8,
+    "penaltyGapOpenInFrame": 9,
+    "penaltyGapOpenOutOfFrame": 10,
+    "penaltyMismatch": 1,
+    "scoreMatch": 5,
+    "retryReverseComplement": true,
+    "allowedMismatches": 10,
+    "minSeedCover": 0.12,
+    "minLength": 100
+  },
+  "qc": {
+    "missingData": {
+      "enabled": true,
+      "missingDataThreshold": 200,
+      "scoreBias": 100
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 4
+    },
+    "frameShifts": {
+      "enabled": true
+    },
+    "stopCodons": {
+      "enabled": true
+    },
+    "privateMutations": {
+      "enabled": true,
+      "cutoff": 150,
+      "typical": 100,
+      "weightLabeledSubstitutions": 1,
+      "weightReversionSubstitutions": 1,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "snpClusters": {
+      "enabled": true,
+      "clusterCutOff": 15,
+      "scoreWeight": 50,
+      "windowSize": 50
+    }
+  }
+}

data/nextstrain/orthohantavirus/andv/l/reference.fasta

@@ -0,0 +1,111 @@
+>NC_003468.2 Andes virus segment L, complete genome
+TAGTAGTAGACTCCGGGATAGAAAAAGTTAGAAAAATGGAAAAGTATAGAGAGATTCATC
+AGAGAGTTAGGGACCTTGCACCTGGAACGGTATCAGCATTAGAATGCATAGATCTACTGG
+ATAGGCTCTACGCTGTCAGACATGACCTGGTTGACCAGATGATAAAACATGACTGGTCTG
+ATAATAAAGATGTAGAAAGACCTATAGGTCAAGTTTTACTGATGGCTGGCATACCTAATG
+ATATTATACAAGGCATGGAGAAGAAGATTATACCAAATAGCCCTTCTGGACAAGTATTGA
+AAAGCTTTTTCCGAATGACACCAGATAATTATAAAATTACAGGTAACTTGATTGAGTTTA
+TTGAAGTGACTGTAACAGCTGATGTGTCACGAGGTATTAGGGAGAAGAAAATAAAGTATG
+AAGGAGGCCTCCAATTTGTTGAGCACTTACTGGAAACTGAATCAAGGAAGGGTAATATAC
+CGCAACCTTATAAAATAACATTCTCAGTGGTTGCAGTTAAAACAGATGGATCAAACATCT
+CGACTCAGTGGCCCAGTCGGAGGAACGATGGGGTAGTTCAGCACATGCGTCTAGTCCAAG
+CTGATATAAATTATGTCAGAGAGCATTTAATAAAGTTAGATGAGAGAGCATCTTTGGAGG
+CAATGTTTAACTTAAAGTTCCATGTATCAGGCCCTAAACTGAGATACTTTAACATCCCTG
+ATTATAGACCACAGCAGCTATGTGAACCACGGATTGACAACTTAATACAATATTGCAAGA
+ATTGGTTGACAAAAGAACATAAGTTTGTATTCAAAGAAGTCAGTGGAGCTAATGTGATTC
+AAGCATTTGAGAGTCATGAACAGTTACATTTACAGAAATACAACGAATCACGAAAACCAA
+GAAATTTTTTACTCTTGCAGCTTACAGTGCAAGGGGCATATCTACCATCAACAATCAGTT
+CTGACCAGTGCAATACTAGGATTGGGTGTCTAGAAATATCAAAAAACCAACCAGAAACAC
+CAGTACAGATGCTTGCATTGGATATATCTTATAAGTATCTGAGTCTTACAAGGGATGAGT
+TGATCAATTATTATAGCCCTAGAGTGCACTTTCAATCGAGCCCTAATGTGAAGGAACCAG
+GGACACTGAAGTTAGGATTATCACAATTAAATCCACTCTCTAAATCAATTCTTGACAATG
+TTGGAAAGCATAAAAAGGATAAAGGATTATTTGGTGAGATCATAGATAGCATAAATGTGG
+CAAGTCAAATACAGATCAATGCATGTGCAAAAATAATTGAGCAGATCTTATCAAATCTTG
+AAATAAACATTGGAGAAATAAATGCTAGTATGCCTTCTCCTAATAAGACAACAGGTGTAG
+ATGACCTGTTAAATAAATTTTATGATAATGAGCTTGGTAAATATATGTTATCCATTCTGA
+GGAAAACAGCAGCATGGCATATAGGCCATCTAGTCAGAGATATCACAGAAAGTTTAATTG
+CACATGCTGGGCTGCGCCGTTCTAAATATTGGTCAGTACATGCATATGACCATGGGAATG
+TAATTTTGTTTATCTTGCCATCAAAGTCACTAGAGGTAGTAGGTTCTTATATAAGGTATT
+TCACAGTATTTAAAGATGGTATAGGGTTGATAGACGCAGATAATATTGATTCTAAGGCCG
+AAATTGATGGTGTCACCTGGTGTTATTCTAAGGTCATGAGTATTGATTTAAACAGGTTAT
+TGGCTTTGAACATAGCTTTTGAGAAGTCACTTCTTGCCACGGCTACATGGTTCCAATATT
+ATACTGAAGACCAAGGCCATTTTCCCCTTCAACATGCATTAAGGTCAATCTTTTCTTTCC
+ACTTTTTACTCTGTGTGTCACAAAAGATGAAGCTATGTGCAATATTTGATAACCTTCGTT
+ATCTGATACCATCAGTAACATCTTTGTACTCTGGGTACGAGTTGTTAATAGAAAAATTCT
+TTGAGAGACCATTTAAGAGTTCACTGGATGTATACCTTTATTCTATCATAAAATCTCTAT
+TAATTAGTTTGGCACAAAATAATAAAGTTCGATTTTACTCAAGAGTTCGTTTGTTAGGAT
+TGACAGTTGATCACTCCACGGTCGGAGCAAGTGGTGTTTACCCCTCTTTAATGTCCCGTG
+TTGTTTACAAACATTACAGAAGTTTAATCTCTGAAGCTACAACTTGTTTTTTCTTATTTG
+AAAAGGGTTTGCATGGGAATTTACCAGAAGAGGCTAAAATACATCTTGAAACCATTGAAT
+GGGCTCGGAAGTTCCAGGAGAAAGAAAAACAATATGGTGATATTCTTCTAAAGGAAGGCT
+ATACAATTGAATCTGTAATCAATGGAGAAGTTGATGTAGAACAACAGCTTTTTTGTCAGG
+AGGTCTCAGAGCTAAGTGCACAAGAGCTCAACAAATATTTACAGGCAAAATCTCAAGTTT
+TATGTGCTAATATCATGAATAAACACTGGGACAAACCATATTTCAGTCAAACACGCAATA
+TCAGTCTCAAGGGAATGTCTGGGGCATTGCAAGAGGATGGACATTTAGCTGCTAGTGTGA
+CACTGATTGAAGCAATTAGGTTTTTAAATAGATCACAAACCAATCCAAATGTTATTGATA
+TGTATGAGCAGACTAAACAATCAAAGGCACAAGCTAGGATTGTTAGGAAATACCAGAGAA
+CAGAAGCAGATAGAGGATTTTTTATCACAACATTACCAACTAGGGTGCGATTAGAAATAA
+TAGAAGATTATTTCGATGCAATTGCAAAGGTTGTGCCTGAAGAATATATTTCTTATGGTG
+GGGATAAAAAAGTTCTAAATATTCAGAATGCACTAGAGAAAGCACTTAGATGGGCATCTG
+GAGTATCAGAAATTACAACAAGCACTGGTAAAAGCATCAAGTTTAAGCGGAAATTAATGT
+ATGTTAGTGCTGATGCCACAAAATGGTCACCAGGAGATAATTCTGCTAAGTTTAGGAGAT
+TTACACAAGCAATATATGATGGCTTATCAGACAACAAACTGAAATGTTGTGTTGTTGATG
+CATTACGTAACATTTATGAGACTGAATTTTTTATGTCCAGGAAATTACACCGATATATTG
+ATAGTATGGAAAATCATTCAGATGCGGTTGAAGATTTCTTGGCATTTTTCTCAAATGGAG
+TCTCAGCCAATGTAAAGGGAAACTGGCTTCAAGGGAACTTAAATAAATGCTCATCATTAT
+TTGGTGCTGCTGTCTCATTACTTTTTCGGGAGGTCTGGAAACAATTGTTTCCAGAATTAG
+AGTGTTTTTTTGAATTTGCACATCATTCAGATGATGCATTGTTCATTTATGGCTATCTGG
+AGCCTGAAGATGATGGAACAGATTGGTTTTTGTATGTATCACAGCAGATACAGGCAGGAA
+ACTTTCATTGGCATGCTATAAATCAAGAGATGTGGAAGAGCATGTTTAATCTACATGAGC
+ACTTACTATTAATGGGTTCTATTAAAGTGTCACCTAAGAAGACAACAGTATCACCTACTA
+ATGCAGAATTTCTTTCTACTTTTTTTGAAGGTTGTGCTGTGTCAATCCCTTTTGTTAAAA
+TCTTACTGGGTTCATTATCAGATCTTCCTGGGTTAGGTTTCTTTGATGATTTAGCAGCAG
+CACAAAGCAGATGTGTAAAGTCACTAGATTTGGGTGCTTGCCCACAATTAGCTCAACTAG
+CTATAGTATTATGCACAAGCAAAGTTGAGAGGTTGTATGGTACTGCTGATGGAATGGTAA
+ACTCTCCAACAGCATTCCTTAAGGTGAATAAAGCACACGTACCAGTACCACTTGGTGGTG
+ATGGCTCAATGTCTATTATGGAGCTTGCAACAGCTGGTTTTGGGATGGCAGATAAGAATA
+TTTTAAAAAATGCATTCATATCTTATAAGCATACTCGTAGAGATGGTGATAGGTACGTAT
+TGGGTTTATTTAAATTTTTGATGTCATTAAGTGAGGATGTATTCCAGCACGACCGATTGG
+GTGAGTTTAGTTTTGTAGGTAAAGTTCAATGGAAAGTGTTCACTCCTAAAGCTGAATTTG
+AATTTCATGATCAATTTTCACATAATTATTTATTAGAGTGGACACGTCAACATCCTGTGT
+ATGACTATATTATTCCTAGAAATAGAGATAATTTGCTTGTATACCTTGTAAGAAAGTTGA
+ATGATCCTAGCATCATTACAGCTATGACTATGCAGTCACCATTACAACTTCGTTTCCGTA
+TGCAAGCAAAGCAACATATGAAAGTATGCCGGTATGAAGGTGAATGGGTCACATTCAGGG
+AGGTACTTGCTGCAGCTGATAGTTTTGCTACGAGTTACCAACCTACTGAAAGGGACATGG
+ATCTCTTTAATACACTTGTAAGTTGTACATTTTCTAAAGAGTATGCTTGGAAAGACTTTT
+TAAATGAAGTAAGGTGTGAGGTCTTAACAACAAGACATGTACATAGGCCTAAAATTGCTA
+GGACATTCACTGTTAGAGAAAAGGACCAGGCTATACAAAATCCAATAAATTCGGTGATTG
+GCTATAAGTATGCTCTTACAGTGGATGAAGTCAGTGATGTTCTTGATAGTGCATTCTTCC
+CAGAGTCTCTATCTGCAGACTTACAGGTTATGAAAGATGGAGTTTACAGAGAATTAGGAC
+TTGATATAAGTTCTCCTGAAGTCCTAAAACGCATAGCACCACTATTATATAAGGCAGGAA
+GGTCACGTGTTGTTATTGTGGAAGGAAATGTAGAAGGGACAGCTGAGTCAATCTGTAGTT
+ATTGGCTCAAGACAATGTCACTGATTAAAACAATCAGAGTAAGACCTAAGAAGGAGGTAC
+TGAAAGCTATGTCTTTATATAGTGTTAAAGAAAATATTGGATTGCAGGATGATATTGCAG
+CAACTCGACTATGCATAGAAATCTGGAGATGGTGTAAGGCAAATGAACAGGATGTTAAAG
+AATGGCTAACATCTCTGTACTTTGAAAAACAGACATTGATGGATTGGGTAGAAAGGTTTA
+GAAGGAAAGGAGTTGTTCCTATTGATCCTGAAATACAATGTATTGGCCTACTCTTATATG
+ATGTATTAGGTTATAAAAGTGTGTTACAAATGCAAGCAAACCGAAGAGCCTATTCAGGTA
+AGCAATATGATGCATACTGTGTGCAAACATATAACGAGGAAACAAAACTATATGAAGGTG
+ACCTTCGTGTTACTTTTAATTTTGGTTTAGATTGTGCAAGGTTAGAAGTTTTTTGGGATA
+AAAAAGAGTATATCTTAGAGACATCTATCACCCAACGACATGTGTTGCGGTTACTGATGG
+AAGAAGTGTCACAAGAATTAATTAGATGTGGAATGAGATTCAAAACAGAGCAAGTCAATC
+AAACTCGGAGCTTAGTGTTATTCAAAACAGAGGCTGGTTTTGAATGGGGTAAGCCTAATG
+TGCCATGTATTGTATATAAACACTGTGTCTTGAGAACTGGGCTTCGTACGAAACAGCCAA
+TTAATAAAGAGTTCATGATAAATGTACAAAGTGATGGTTTCCGTGCAATAGCACAGATGG
+ATATTGAGAGTCCACGGTTCTTGTTAGCACATGCATATCATACACTGCGTGATATTAGAT
+ATCAAGCAGTGCAGGCAGTAGGGAATGTATGGTTTAAAACAGAACAGCACAAACTATTTA
+TTAACCCAATTATATCATCAGGGCTTTTAGAAAACTTTATGAAAGGCTTACCTGCTGCCA
+TACCTCCTGCTGCATATTCCCTCATAATGAACAAGGCTAAGATTTCTGTGGATTTGTTTA
+TGTTCAATGAGCTATTAGCACTTATAAATAGGAATAATATCCTCAACCTTGATGGGATTG
+AAGAAACATCTGAAGGTTATAGTACTGTGACATCAATGTCTAGCAAGCAGTGGTCTGAAG
+AGATGAGTTTAATGTCTGATGATGATATTGATGATATGGAGGACTTTACTATAGCACTGG
+ATGATATTGACTTTGAACAAATAAATTTGGAAGAGGATATACAACACTTTCTGCAGGATG
+AATCAGCATATGTTGGTGATTTATTGATTCAGACAGAAGACATTGAGGTTAAAAAGATAC
+GTGGGGTGACAAGAGTATTAGAGCCAGTCAAGCTATTAAAAAGCTGGGTTTCTAAAGGCC
+TTGCTATAGACAAAGTATACAATCCTATCGGGATAATCTTAATGGCAAGATACATGTCAA
+AAACATACAATTTCAGTTCAACACCTCTTGCACTATTAAATCCATATGACTTGACAGAAC
+TTGAAAGTGTTGTAAAGGGATGGGGAGAAACTGTAAATGATCGATTCAAAGATTTAGATA
+TTGAGGCACAAACAGTTGTTAAAGAAAAGGGTGTACAGCCAGAAGATGTACTCCCTGATT
+CATTATTCTCTTTCAGGCATGTTGATGTTTTGCTGCGAAGGTTGTTCCCGCGTGACCCTG
+TATCAACATTCTATTAGTGGATTTTATACCTTATTCATACAGTATGTATATTGTAGTGTT
+CTTTTCCCGGAGCATACTACTA