From 7c1c6105f54761762f3c071428a1083845904754 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Laboratoire=20des=20Maladies=20Infectieuses=20Virales=20V?= =?UTF-8?q?=C3=A9t=C3=A9rinaires?= Date: Wed, 10 Jun 2026 10:06:33 -0400 Subject: [PATCH 1/4] Create reference.fasta --- .../PRRSV2/nsp3-4-5/Baby2026/reference.fasta | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/reference.fasta diff --git a/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/reference.fasta b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/reference.fasta new file mode 100644 index 000000000..97bc499cc --- /dev/null +++ b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/reference.fasta @@ -0,0 +1,32 @@ +>NC_038291.1-nsp3-4-5 +GGAGGCCCACATCTCATGGCTGCCCTGCATGTTGCCTGCTCGATGGCTCTGCACATGCTT +GCTGGGATTTATGTGACTGCGGTGGGTTCTTGCGGCACCGGCACCAACGACCCGTGGTGC +GCTAACCCGTTTGCCGTCCCTGGCTACGGACCTGGCTCTCTCTGCACGTCCAGGTTGTGC +ATTTCCCAACACGGCCTTACCCTGCCCTTGACAGCACTTGTGGCGGGATTCGGTATTCAA +GAAATTGCCTTGGTCGTTTTGATTTTTGTTTCCATCGGAGGCATGGCTCATAGGTTGAGC +TGTAAGGCTGACATGCTGTGTGTTTTGCTTGCAATTGCCAGCTATGTTTGGGTACCTCTT +ACCTGGTTGCTTTGTGTGTTTCCTTGCTGGTTGCGCTGTTTTTCTTTGCACCCCCTCACC +ATCCTATGGTTGGTGTTTTTCTTGATTTCTGTGAATATGCCTTCAGGAATCTTGGCCATG +GTGTTGTTGGTTTCTCTTTGGCTTCTTGGTCGTTATACTAATGTTGCTGGCCTTGTCACC +CCCTACGACATTCATCATTACACCAGTGGCCCCCGCGGTGTTGCCGCCTTGGCTACCGCA +CCAGATGGGACCTACTTGGCCGCTGTCCGCCGCGCTGCGTTGACTGGCCGCACCATGCTG +TTTACCCCGTCCCAGCTTGGGTCTCTTCTTGAGGGTGCTTTCAGAACTCGAAAGCCCTCA +CTGAACACCGTCAATGTGATCGGGTCCTCCATGGGCTCTGGCGGGGTGTTTACCATCGAC +GGGAAAGTCAAGTGCGTAACTGCCGCACATGTCCTTACGGGCAATTCAGCTCGGGTTTCC +GGGGTCGGCTTCAATCAAATGCTTGACTTTGACGTAAAGGGAGATTTCGCTATAGCTGAT +TGCCCGAATTGGCAAGGGGCTGCCCCCAAGACCCAATTCTGCACGGATGGATGGACTGGC +CGTGCCTATTGGCTAACATCCTCTGGCGTCGAACCCGGCGTCATTGGAAAAGGATTCGCC +TTCTGCTTCACCGCATGTGGCGATTCCGGGTCCCCAGTGATCACCGAGGCCGGTGAGCTT +GTCGGCGTTCACACGGGATCGAATAAACAAGGGGGGGGCATTGTTACGCGCCCCTCAGGC +CAGTTTTGTAATGTGGCACCCATCAAGCTAAGCGAATTAAGTGAATTCTTTGCTGGGCCT +AAGGTCCCGCTCGGTGATGTGAAGGTCGGCAGCCACATAATTAAAGACATAAGCGAGGTG +CCTTCAGATCTTTGTGCCTTGCTTGCTGCCAAACCTGAACTGGAAGGAGGCCTCTCCACC +GTCCAACTTCTTTGTGTGTTTTTTCTCCTGTGGAGAATGATGGGACATGCCTGGACGCCC +TTGGTTGCTGTGAGTTTCTTTATTTTGAATGAGGTTCTCCCAGCCGTCCTGGTCCGGAGT +GTTTTCTCCTTTGGAATGTTTGTGCTATCCTGGCTCACGCCATGGTCTGCGCAAGTTCTG +ATGATCAGGCTTCTGACAGCAGCTCTTAACAGGAACAGATGGTCACTTGCCTTTTTCAGC +CTCGGTGCAGTGACCGGTTTTGTCGCAGATCTTGCGGCCACTCAGGGGCATCCGTTGCAG +GCAGTGATGAATTTGAGCACCTATGCATTCCTGCCTCGGATGATGGTTGTGACCTCACCA +GTCCCAGTGATCACGTGTGGTGTCGTGCACCTACTTGCCATCATTTTGTACTTGTTTAAG +TACCGTGGCCCGCACCATATCCTTGTTGGCGATGGAGTGTTCTCTGCGGCTTTCTTCTTG +AGATACTTTGCCGAG From de88723580366e7b17b0a86dfd440dcb4c5e2b81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Laboratoire=20des=20Maladies=20Infectieuses=20Virales=20V?= =?UTF-8?q?=C3=A9t=C3=A9rinaires?= Date: Wed, 10 Jun 2026 10:06:56 -0400 Subject: [PATCH 2/4] Add files via upload --- .../PRRSV2/nsp3-4-5/Baby2026/CHANGELOG.md | 3 + .../BabyV/PRRSV2/nsp3-4-5/Baby2026/README.md | 24 + .../nsp3-4-5/Baby2026/genome_annotation.gff3 | 4 + .../PRRSV2/nsp3-4-5/Baby2026/pathogen.json | 53 + .../PRRSV2/nsp3-4-5/Baby2026/sequences.fasta | 256 + .../BabyV/PRRSV2/nsp3-4-5/Baby2026/tree.json | 111575 +++++++++++++++ 6 files changed, 111915 insertions(+) create mode 100644 data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/CHANGELOG.md create mode 100644 data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/README.md create mode 100644 data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/genome_annotation.gff3 create mode 100644 data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/pathogen.json create mode 100644 data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/sequences.fasta create mode 100644 data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/tree.json diff --git a/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/CHANGELOG.md b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/CHANGELOG.md new file mode 100644 index 000000000..40410d5c0 --- /dev/null +++ b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/CHANGELOG.md @@ -0,0 +1,3 @@ +## Unreleased + +Initial release. \ No newline at end of file diff --git a/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/README.md b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/README.md new file mode 100644 index 000000000..70c978c08 --- /dev/null +++ b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/README.md @@ -0,0 +1,24 @@ +# Betaarterivirus americense (PRRSV-2) nsp3-4-5 classification + + +## Dataset attributes + +| attribute | value | +| -------------------- | ---------------------------------------- | +| name | PRRSV-2 nsp3-4-5 clusters | +| refName | NC_038291.1-VR-2332 | +| refAccession | NC_038291.1 | + + +## Scope of this dataset + +This dataset uses the sequences of the ORF1 non structural protein 3, 4 and 5 to complement the ORF5 lineages classification when the whole genome of the virus is available as proposed by Baby et al., 2026. + + +## Authors and contacts + +For questions regarding the dataset, please contact the corresponding author of + +## What is Nextclade dataset + +Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/genome_annotation.gff3 b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/genome_annotation.gff3 new file mode 100644 index 000000000..6626d4faa --- /dev/null +++ b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/genome_annotation.gff3 @@ -0,0 +1,4 @@ +##gff-version 3 +##sequence-region NC_038291.1-nsp3-4-5 1 1815 +NC_038291.1-nsp3-4-5 feature CDS 1 1815 . + 0 Parent=gene-ORF1;gene_name=nsp3-4-5;product=nsp3-4-5 +NC_038291.1-nsp3-4-5 feature gene 1 1815 . + . ID=gene-ORF1;gene_name=ORF1;Note=Partial ORF1 diff --git a/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/pathogen.json b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/pathogen.json new file mode 100644 index 000000000..de9122924 --- /dev/null +++ b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/pathogen.json @@ -0,0 +1,53 @@ +{ + "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json", + "schemaVersion": "3.0.0", + "files": { + "reference": "reference.fasta", + "pathogenJson": "pathogen.json", + "genomeAnnotation": "genome_annotation.gff3", + "examples": "sequences.fasta", + "treeJson": "tree.json", + "readme": "README.md", + "changelog": "CHANGELOG.md" + }, + "attributes": { + "name": "Betaartivirus americense nsp3-4-5 classification", + "reference name": "NC_038291.1-nsp3-4-5", + "reference accession": "NC_038291.1" + }, + "qc": { + "missingData": { + "enabled": false, + "missingDataThreshold": 2000, + "scoreBias": 300 + }, + "snpClusters": { + "enabled": false, + "windowSize": 100, + "clusterCutOff": 5, + "scoreWeight": 50 + }, + "privateMutations": { + "cutoff": 25, + "enabled": true, + "typical": 10, + "weightLabeledSubstitutions": 2, + "weightReversionSubstitutions": 1, + "weightUnlabeledSubstitutions": 1 + }, + "mixedSites": { + "enabled": true, + "mixedSitesThreshold": 8 + }, + "frameShifts": { + "enabled": true + }, + "stopCodons": { + "enabled": true + } + }, + "compatibility": { + "cli": "3.0.0", + "web": "3.0.0" + } +} \ No newline at end of file diff --git a/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/sequences.fasta b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/sequences.fasta new file mode 100644 index 000000000..e04b2b6e8 --- /dev/null +++ b/data/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/sequences.fasta @@ -0,0 +1,256 @@ +>MN046230.1 +GGAGGCCCACACCTCGCAGCTGCTCTGCATGTTGCCTGCTCGATGACCTTGCACATGCTT +GCTGGAATCTATGTGACCTCGGTGAGCACCTGCGGCACCGGCACCAATGACCCGTGGTGC +ACCAATCCGTTTGCCGTCCCTGGTTACGGACCCGGCTCTCTCTGCACGTCTAGGTTGTGC +ATCTCCCAGCATGGCCTTACACTGCCCTTGACGGCGTTGGTGGCCGGTTTCGGCATTCAG +GAAGTCGCTTTGGTTGTTTTAATCTTAATTTCCATCGGTGGCTTGGCTCACCGGTTGAGT +TGCAAGGCTGATGTGATGTTTGTTTTACTCGCAATCGCTTGCTATGTTTGGGAACCTCTC +ACCTGGTTGCTTTGTGTGTTTCCTTGCTGGCTGCGGTATTTTTCTTTGCACCCTTTCACT +ATTCTATGGTTAGTGTTTTTCTTGATCGCTGTAAACGCGCCTTCGGGGATCTTAGCCTTG +GTGTTGTTGGTCGTTCTTTGGCTCCTCGGCCGCTATACCAATGTTGCTGGTCTTGTCACC +CCCTATGACATCCACCATTACACCAATGGCCCCCGTGGTGTTGCTGCCTTGGCCACCGCA +CCGGAAGGAACCTACCTGGCCGCTGTCCGCCGCGCCGCGTTGACTGGTCGCACCATGCTG +TTCACCCCGTCTCAGCTTGGGTCCCTCCTTGAGGGTGCTTTCAGAACTCAAAAGCCCTCA +CTGAATACCGTCAATGTGGTCGGGTCCTCCATGGGCTCTGGCGGAGTGTTCAATATTGAC +GGGAAAATCAAGTGCGTGACTGCCGCACATGTCCTTACGGGTAACTCAGCTAGGGTTTCC +GGGGTCGGCTTTAATCAGATGCTTGACTTTGATGTAAAAGGGGACTTCGCCATAGCTGAT +TGCCCGAATTGGCAAGGAGTTGCTCCCAAGGCCCAGTTCTGTAAGGATGGGTGGACTGGC +CGCGCCTATTGGCTGACATCTTCTGGCGTTGAACCCGGTGTTATTGGGAATGGGTTCGCC +TTCTGCTTCACCGCGTGTGGTGATTCTGGATCCCCAGTGATTACCGAAGCCGGTGAGCTT +GTCGGCGTTCATACAGGGTCAAACAAACAAGGAGGAGGCATTGTCACGCGCCCCTCAGGC +CAGTTTTGTAATGTGAAGTCCATCAAGCTGAGCGAATTGAGTGAATTCTTCGCTGGACCC +AAGGTCCCGCTCGGTGATGTAAAACTCGGCAGTCACATAGTTAAAGACACACACGAGGTG +CCTTCAGATCTTTGTGCCCTGCTTGCTGCCAAACCTGAACTGGAAGGAGGTCTTTCCACA +GTTCAACTTCTGTGTGTGTTTTTCCTCCTGTGGAGGATGATGGGGCATGCCTGGACGCCT +TTGGTTGCTGTGGGGTTTTTCCTCCTGAATGAGATTCTCCCAGCTGTCCTGGTCCGGAGT +GCTTTCTCCTTCGGGATGTTTGTGCTGTCCTGGCTCACGCCATGGTCTGCGCAAGTCCTG +ATGATCAGGCTTCTGACAGCAGCCCTTAACAGAAACAAATTGTCTCTTGGTTTTTACAGC +CTTGGGGCAATAACCAGTTTTGTCGCAGACCTTGCGGTGACTCAAGGGCGCCCGTTACAG +GTGGTAATGAACCTGAGCACTTATGCCTTCTTGCCCCGAATGATGGTTGTGTCCTCACCA +GTCCCGGTGATCGCTTGCGGCGTCGTGCACCTCCTTGCCATAATTTTGTACTTGTTTAAG +TACCGCTGTCTTCATAATGTCCTTGTTGGCGATGGAGCATTCTCTTCGGCTTTTTTTTTG +CGATACTTTGCCGAG +>ON365556.1 +GGAGGCCCACACCTCATTGCTGCCTTGCATGTTGCTTGCTCGATGGCTCTTCACATGCTT +GCCGGGATTTATGTGACCTCGGTGAGCACCTGCGGCACTGGCACTAACGACCCGTGGTGT +ACCAATCCGTTTGCCGTCCCTGGTTACGGACCCGGCTCACTCTGCACGTCTAGGTTGTGT +ATCTCCCAGCATGGCCTCACACTACCCTTGACGGCGCTAGTGGCTGGGTTCGGTATTCAG +GAGATTGCTTTGGTTGTTTTAATCTTTGTTTCTATCGGTGGTTTGGCTCATCGGTTGAGT +TGCAAGGCTGACATGTTGTGCATCTTACTCGCAATCGCTAGTTATGTTTGGGAACCTCTC +ACTTGGTTGCTTTGTGTGTTTCCTTGTTGGCTGCGGTGTTTTCCTTTGCATCCTTTCACC +GTTCTATGGTTGGTGTTTTTCTTGATCTCTGTAAATGCGCCTTCGGGGATTTTGGCTGTG +GTGTTATTGGTTTCCCTCTGGCTTTTAGGTCGTTATACTAACATTGCTGGTCTTGTCACC +CCCTACGACATTCATCATTACACCAGCGGCCCTCGCGGCGTCGCCGCCTTGGCTACCGCA +CCAGATGGAACCTACTTGGCTGCCGTTCGCCGTGCTGCGTTGACTGGTCGTACCATGCTA +TTCACCCCGAGTCAACTCGGGTCCCTTCTTGAGGGCGCTTTCAGAACCCAAAAGCCCTCA +TTGAACACTGTCAATGTGGTTGGGTCCTCTATGGGCTCTGGCGGAGTGTTCACTATTGAC +GGGAAAATCAAGTGCGTGACTGCCGCACATGTCCTTACGGGTAACTCAGCTAGGGTTTCC +GGGGTCGGCTTTAACCAGATGCTTGACTTTGATGTAAAGGGGGACTTTGCCATAGCTGAT +TGCCCGAACTGGCAAGGGGCTGCTCCTAAGACCCAGTTTTGCAAGGATGGGTGGACTGGT +CGCGCCTACTGGCTGACATCCTCTGGCGTTGAGCCTGGCGTCATTGGAAATGGGTTCGCC +TTCTGCTTCACCGCGTGCGGCGATTCTGGATCTCCAGTGATCACTGAAGCCGGTGAGCTT +GTTGGTGTTCACACAGGATCAAACAAACAAGGAGGAGGCATTGTTACGCGCCCCTCGGGC +CAGTTTTGTAATGTGACTCCTGTCAAGCTGAGCGAGTTGAGTGAATTTTTCGCTGGACCT +AAGGTCCCGCTTGGTGACGTGAAGATTGGTAATCACATAATTAAGGATGCATGTGAGGTG +CCTTCGGACCTTTGTGCCCTGCTTGCTGCCAAACCCGAACTGGAAGGAGGCCTCTCCACA +GTTCAACTTCTGTGTGTGTTTTTCCTCCTGTGGAGAATGATGGGACATGCCTGGACACCC +CTGGTCGCTGTGGGATTTTTTATCCTGAATGAGATACTTCCAGCGGTGCTGGTCCGGAGT +GTTTTCTCCTTTGGGATGTTTGCACTATCTTGGTTCACGCCATGGTCTGCACAAGTCCTA +ATGATCAGACTTCTCACAGCATCCCTTAACAGAAACCAATTGTCTCTTGTTTTTTACAGC +CTTGGTGCAATAACCGGCTTTGTCGCAGATCTTGCGGTGACTCAAGGGAATCCGTTACAG +GTGGTAATGAACCAGAGCACTTATGCCTTCCTGCCTCGGGTGATGGTTGTGACCTCACCA +GTCCCAATGATTACGTGTGGTGTTGTGCACCTTCTTGCCATAATCTTGTACTTGTTTAAG +TACCGCTGCCTTCACCATGTTCTCGTTGGCGACGGAGTGTTCTCTGCGGCTTTCTTCTTG +CGATATTTTGCCGAG +>MN865490.1 +GGGGGTCCACACCTCATGGCGGCCTTACACGTTGCCTGCTCGATGACCTTGCACATGCTT +GTTGGGATTTATGTCACCACGGTGGGCTCTTGTGGTTCAGGCACTAACGATCCGTGGTGC +ACCAACCCGTTTGCTGTCCCTGTCTATGGACCTGGCTCTCTTTGCACGTCCAGGCTGTGC +ATTTCCCAGCATGGTCTTACCCTGCCTTTGACAGCGTTTGTGGCTGGATTTGGCATTCAG +GAAATTGCCATGGTGGTTTTAATCTTTGTTTCCATCGGGGGTATGGCTCACAGGTTGAGT +TGCAAAGCTGATGTGTTGTGTGTTCTGCTTGCGATAGCTAGCTATGTTTGGGAGCCCCTC +ACCTGGTTGCTCTGCACATTTCCTTGCTGGTTGCGCTGGTTTTCTCTGCATCCCCTTACC +ATCTTATGGCTGGTGTTTTTCTTAATCTCTATGAACATGCCTTCAGGAATTTTGGCCTTG +GTGTTGTTGATCTCTTTCTGGCTCCTTGGTCGTTACACTAATGTTGCCGGCCTTGTCACC +CCCTACGACATTCACCATTACACCAACGGCCCCCGCGGCGTTGCCGCCTTGGCCACCGCG +CCGGACGGGACCTACTTGGCCGCTGTCCGCCGCGCAGCGTTGACCGGTCGCACCATGTTG +TTTACCCCGTCTCAATTAGGATCACTCCTAGAGGGCGCCTTTAGAACTCAAAAGCCCGCA +CTGAATACTGTCAACGTGGTTGGGTCCTCCATGGGCTCCGGCGGGGTGTTCACCATTGAC +GGGAAGATCAAATGCGTGACCGCCGCACATGTTCTCACGGGCAACTCTGCCAGAGTCTCC +GGGATTGGCTTCAACAAAATGTTGGACTTCGATGTGAAAGGGGATTTTGCTATAGCAGAT +TGCCCGGATTGGCAAGGAGCCGCCCCGAGAACCCAATTTTGCACGGATGGCTGGACTGGC +CGCGCTTATTGGCTAACGTCCTCTGGTGTCGAACCTGGCGTCATTGGGGAAGGGTTCGCC +TTCTGTTTTACCGCGTGCGGCGACTCTGGTTCCCCAGTGATCACCGAGGCCGGGGAGCTT +GTCGGTGTCCACACGGGATCAAATAAACAAGGAGGAGGCATCGTCACGCGCCCTTCAGGC +CAGTTTTGTAATGTGACACCCGTCAAATTAAGTGAATTAAGTGAATTCTTCGCTGGACCC +AGGGTCCCACTCGGTGATGTGAAGGTCGGCAGCCATGTGATTAAAGATGTAAATGAGGTG +CCCTCAGATCTTTGCGCCTTGCTTGCTGCCAAACCCGAGTTGGAAGGGGGCCTCTCCACC +GTCCAACTTTTGTGCGTGTTTTTTCTCCTATGGAGAATGATGGGGCATGCCTGGACGCCC +TTGGTTGCTGTCGGGTTTTTTGTCTTGAATGAAATCCTCCCAGCAGTTTTGGTCCGGAGT +GTTTTCTCCTTTGGTATGTTTGCGCTGTCTTGGTTCACGCCGTGGTCTGCGCAAATTCTG +ATGATTAGGCTTTTAACCGCAGCTCTTAACAGGACCAAGTTGTCACTTGCTGTTTACAGT +CTTGGTGCGCTGACTGGATTTGTTGCGGAAGTTGCAACCAATCAGGGGCGGTCGTTACAC +GCGATCATGAACTTGAGCACCTATGCATTCCTGCCTCGTGCAATGGCCATGGCCTCACCA +GTCCCAATAATTGCGTGTGGTGTCGTGCACTTGCTTGCTATTGTTATGCACTTGTTCAAG +TACCGTAGCTTGCATGCCGTTCTGGTTGGCGATGGTGCGTTCTCCGCGGCTTTCTTCTTG +CGATACTTTGCGGAG +>KT257956.1 +GGAGGTCCACACCTCATGGCGGCTCTACATGTCGCTTGCTCAATGGCTTTGCACATGCTT +ATCGGAATTTATGTAACTGCGGTGGGTTCTTGCGGTTCTGGTACCAGTGATCCGTGGTGC +ACTAACCCGTTTGCCGTCCCTGTCTACGGACCTGGTTCTCTCTGCACGTCCAGGTTATGT +ATCTCCCAGCACGGCCTTACCTTGCCCTTAACAGCGCTTGTGGCAGGGTTTGGCTTTCAG +GAAATTGCCTTGGTTGTTTTAATCTTTGTCTCCATTGGGGGCATGGCCCACAGATTAAGT +TGCAAGGCTGATGTGTTGTGTGTTCTACTTGCAATTGCCAGCTATGTTTGGGTGCCTCTC +ACCTGGTTGCTCTGCGTGTTTCCTTGCTGGCTGCGCTGGTTCTCTCTGCATCCCCTCACC +ATTCTATGGCTGGTGTTTTTCTTGGTCTCTGTAAATATGCCCTCAGGAATCTTGGCCTTG +GTGTTGCTAATCTCTCTTTGGCTCCTTGGTCGCTACACCAATGTTGCCGGCCTTGTCACC +CCGTACGATATTCACCATTACACCAACGGCCCCCGCGGTGTGGCCGCCTTAGCCACTGCA +CCGGATGGGACTTACCTGGCCGCTGTCCGTCGCGCAGCGTTGACCGGTCGCACCATGCTG +TTCACCCCGTCTCAATTGGGGTCACTCCTTGAGGGTGCCTTTAGAACTCAAAAGCCCTCA +CTGAATACTGTCAATGTGGTTGGGTCCTCCATGGGCTCCGGCGGGGTGTTCACCATTGAC +GGGAAGATCAAATGTGTGACTGCCGCACATGTCCTTACGGGTAACTCTGCCAGAGTCTCC +GGGGTTGGCTTCAATCAAATGCTGGACTTCGATGTGAGAGGGGATTTTGCTATAGCCGAC +TGTCCGGATTGGCAAGGAGTCGCTCCGAAAACCCAATTCTGCAAGGATGGCTGGACAGGC +CGCGCTTATTGGCTAACGTCCTCTGGCGTTGAGCCTGGTGTCATTGGGAATGGATTCGCC +TTTTGTTTCACCGCGTGTGGCGATTCTGGTTCCCCAGTGATCACCGAGGCCGGGGAGCTT +GTTGGTGTTCATACGGGGTCAAACAAACAAGGAGGAGGCATTGTTACGCGCCCTTCAGGC +CAGTTTTGTGATGTGACGCCCACCAAACTGAGTGAATTGAGTGAATTCTTTGCCGGACCC +AGAGTTCCACTTGGTGATGTAAAGGTTGGCAACCACATAATTAAAGATACAAATGAGGTG +CCCTCAGATCTTTGCGCCTTGCTTGCTGCCAAGCCTGAATTGGAGGGGGGCCTCTCCACC +GTCCAACTTTTGTGCGTATTTTTCCTCCTATGGAGGATGATGGGACATGCCTGGACGCCC +TTAGTTGCCGTTGGCTTTTTTGTCTTGAATGAAATCCTCCCAGCAGTCTTGGTCCGGAGT +GTTTTCTCTTTTGGCATGTTCGCACTGTCTTGGTTCACGCCGTGGTCTGCACAAATTCTG +ATGATCAGGCTCCTAGCTGCAGCTCTTAACAGGAACAGGTGGTCACTTGCTTTTTATAGC +CTTGGTGCGCTGACCGGATTTGTTGCGGATCTTGCAGTTAATCAGGGGTGGTCGTTGCAC +GCGGTCATGAATTTGAGCACTTATGCATTTTTGCCTCGTGCAATGGTCACGGTTTCACCA +GTCCCGATAATTGCGTGCGGTGTTGTGCACTTGCTTGCTATCATTTTGTACTTGTTCAAG +TACCGCAGCCTGCATGCTGTCCTAGTTGGCGATGGCGCGTTCTCCGCAGCTTTCTTTTTG +CGATACTTTGCGGAA +>KP283406.1 +GGAGGTCCACACATCATGGCGGCCTTACATGTCGCTTGCTCGATGGCTTTGCACATGCTT +GTTGGGATTTATGTCACTGCGGTGGGTTCTTGCGGTTCTGGCACTAACGACCCGTGGTGC +ACTAACCCGTTTGCCGTCCCTGTCTACGGACCTGGCTCTCTTTGCACCTCCAGGTTGTGC +ATCTCCCAGCATGGCCTTACTCTGCCCTTAACAACGCTTGTGGCGGGGTTTGGCATTCAG +GAAGTTGCCCTGGTGGTTTTAATCTTTGTTTCCATCGGAGGTATGGCTCACAGATTAAGT +TGCAAGGCTGATGTACTGTGCATTCTGCTTGCGATTGCCAGCTATGTTTGGTTACCCCTC +ACCTGGTTGCTCTGTGTGTTTCCTTGCTGGTTACGTTGGTTTTCTTTGCATCCCCTCACC +GTTACATGGTTGGTGTTTTTCTTGATTTCTGTAAACATGCCCTCAGGAGTCTTGGCCTTG +GTATTGTTAATCTCTCTCTGGCTCCTTGGTCGCTATACCAATGTCGCAGGTCTTGTCACT +CCTTATGACATTCACCATTACACCAACGGCCCCCGCGGCGTCGCCGCCTTGGCCACTGCA +CCGGATGGGACCTACTTGGCTGCTGTCCGCCGCGCTGCGCTGACTGGTCGCACCATGCTG +TTTACCCCGTCCCAGCTTGGGTCACTCCTTGAGGGTGCCTTTAGAACCCAAAAGCCTACA +TTGAACACCGTCAATGTGGTCGGGTCCTCTATGGGCTCCGGCGGGGTGTTCACCATTGAC +GGGAAAACCAAGTGCGTAACAGCGGCGCATATTCTCACGGGCAACTCTGCCAGGGTCTCC +GGGATCGGCTTTAATCAAATGTTGGATTTCGATGTGAAAGGGGATTTTGCCATAGCCGAT +TGTCCGAATTGGCAAGGAGTCGCTCCCAAGTCCCAGTTTTGTGAGGATGGGTGGACGGGT +CGCGCTTATTGGCTAACATCCTCTGGCGTCGAACCCGGCGTCATTGGGAGAGGATTTGCC +TTTTGTTTCACCGCGTGCGGCGACTCCGGGTCCCCAGTGATCACCGAGGCCGGAGAACTT +GTCGGTGTCCACACGGGATCAAACAAACAAGGAGGAGGCATTGTCACGCGCCCTTCAGGC +CAGTTTTGTAATGTGACACCTACCAAACTGAGTGAATTGAGTGAATTCTTCGCTGGACCC +AAAGTCCCACTTGGCGATGTGAAGGTCGGTAACCATATAATCAAAGACACAAATGAGGTG 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+ ] + } + ] + } + ] + } + ] + } + ] + } + ] + } +} \ No newline at end of file From 13a7146ab828da3cf8ebde54177a93c34e1e2b65 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Wed, 10 Jun 2026 18:21:40 +0200 Subject: [PATCH 3/4] chore: exclude dataset.zip from git archives - `export-ignore` prevents redundant pre-built zip bundles from appearing in `git archive` output (used by GitHub releases and Zenodo) - Reduces Zenodo archive size from ~496 MB to ~252 MB per release - `dataset.zip` contents are identical to the loose files already in each dataset version directory --- .gitattributes | 1 + kb/reports/zenodo-storage.md | 53 ++++++++++++++++++++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 .gitattributes create mode 100644 kb/reports/zenodo-storage.md diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 000000000..3e747863f --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +data_output/**/dataset.zip export-ignore diff --git a/kb/reports/zenodo-storage.md b/kb/reports/zenodo-storage.md new file mode 100644 index 000000000..d43745ddf --- /dev/null +++ b/kb/reports/zenodo-storage.md @@ -0,0 +1,53 @@ +# Zenodo Storage for nextclade_data: Status and Optimization + +## Background + +The `nextclade_data` repository is archived on Zenodo via GitHub integration. Each GitHub release automatically creates a new Zenodo version under concept DOI [10.5281/zenodo.17880000](https://zenodo.org/records/20446446). The archive is a full `git archive` snapshot of the repository. + +## Current Storage Footprint + +- 17 versions archived since Dec 2025 +- ~496 MB per version (latest), growing from 418 MB over 7 months +- 8.0 GB cumulative across all versions +- ~12 GB/year projected at current release cadence (~24 releases/year) + +All 17 existing versions are permanent -- Zenodo does not allow deletion after 30 days. + +## Cost + +Zenodo is free, funded by CERN and EU grants. Data is stored in CERN data centres (Geneva + Budapest), backed up to tape nightly, retained for the lifetime of CERN (20+ years). No paid tier exists. + +Current limits: 50 GB per record, 100 files per record, 150 GB account-level quota. We are well within limits but consuming storage at a pace that adds up over years. + +## What's in the 496 MB + +The archive is dominated by `data_output/`, the built dataset server directory (3.8 GB uncompressed, ~460 MB compressed). Within it: + +| Content | Uncompressed | Share of archive | +| ---------------------------------- | ------------ | ---------------- | +| `dataset.zip` (pre-built bundles) | 1.9 GB | ~48% | +| `tree.json` (phylogenetic trees) | 1.3 GB | ~33% | +| `sequences.fasta` (examples) | 579 MB | ~12% | +| Other (configs, refs, annotations) | ~170 MB | ~7% | + +The `dataset.zip` files are fully redundant -- each bundles the same loose files (`tree.json`, `pathogen.json`, `reference.fasta`, etc.) already present in the same directory. + +## Accepted Optimization + +Exclude `dataset.zip` from `git archive` via `.gitattributes`. + +A single line in `.gitattributes` at the repository root: + +``` +data_output/**/dataset.zip export-ignore +``` + +This tells `git archive` (used by GitHub and Zenodo to produce release archives) to skip all `dataset.zip` files. Normal git operations (clone, pull, push) are unaffected. + +Verified result: archive size drops from 473 MB to 252 MB, a 47% reduction. Projected annual Zenodo consumption drops from ~12 GB to ~6 GB. + +## Future Opportunity: Delta-only Releases + +Analysis of recent releases shows that typical releases change only 1-3 datasets, producing deltas of 0.3-1 MB compressed. Even SC2 updates (the heaviest) produce ~35 MB deltas. A custom upload script using the Zenodo REST API could upload only changed datasets instead of full snapshots, reducing per-release storage by 90-99%. This would require replacing the automatic GitHub-Zenodo integration with a CI script (~4-5 HTTP calls via `curl`/`jq`). + +This option is deferred but remains available if storage growth warrants it. From 0946feeeefeeb6b9c72aff4782697d79b1958e8e Mon Sep 17 00:00:00 2001 From: nextstrain-bot Date: Mon, 22 Jun 2026 09:09:31 +0000 Subject: [PATCH 4/4] chore: rebuild [skip ci] --- data/community/collection.json | 3 +- .../nsp3-4-5/Baby2026/unreleased/CHANGELOG.md | 3 + .../nsp3-4-5/Baby2026/unreleased/README.md | 24 + .../nsp3-4-5/Baby2026/unreleased/dataset.zip | Bin 0 -> 19785981 bytes .../unreleased/genome_annotation.gff3 | 4 + .../Baby2026/unreleased/pathogen.json | 60 + .../Baby2026/unreleased/reference.fasta | 32 + .../Baby2026/unreleased/sequences.fasta | 256 + .../nsp3-4-5/Baby2026/unreleased/tree.json | 111575 +++++++++++++ data_output/index.json | 42 + data_output/minimizer_index.json | 126998 ++++++++------- 11 files changed, 175661 insertions(+), 63336 deletions(-) create mode 100644 data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/CHANGELOG.md create mode 100644 data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/README.md create mode 100644 data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/dataset.zip create mode 100644 data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/genome_annotation.gff3 create mode 100644 data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/pathogen.json create mode 100644 data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/reference.fasta create mode 100644 data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/sequences.fasta create mode 100644 data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/tree.json diff --git a/data/community/collection.json b/data/community/collection.json index fe58fbd20..7851c3d7d 100644 --- a/data/community/collection.json +++ b/data/community/collection.json @@ -44,6 +44,7 @@ "community/itps/orov/M/tefe", "community/itps/orov/L/tefe", "community/itps/orov/S/tefe", - "community/itps/orov/S/refseq" + "community/itps/orov/S/refseq", + "community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026" ] } diff --git a/data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/CHANGELOG.md b/data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/CHANGELOG.md new file mode 100644 index 000000000..40410d5c0 --- /dev/null +++ b/data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/CHANGELOG.md @@ -0,0 +1,3 @@ +## Unreleased + +Initial release. \ No newline at end of file diff --git a/data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/README.md b/data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/README.md new file mode 100644 index 000000000..70c978c08 --- /dev/null +++ b/data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/README.md @@ -0,0 +1,24 @@ +# Betaarterivirus americense (PRRSV-2) nsp3-4-5 classification + + +## Dataset attributes + +| attribute | value | +| -------------------- | ---------------------------------------- | +| name | PRRSV-2 nsp3-4-5 clusters | +| refName | NC_038291.1-VR-2332 | +| refAccession | NC_038291.1 | + + +## Scope of this dataset + +This dataset uses the sequences of the ORF1 non structural protein 3, 4 and 5 to complement the ORF5 lineages classification when the whole genome of the virus is available as proposed by Baby et al., 2026. + + +## Authors and contacts + +For questions regarding the dataset, please contact the corresponding author of + +## What is Nextclade dataset + +Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/dataset.zip b/data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/dataset.zip new file mode 100644 index 0000000000000000000000000000000000000000..67d22bb529df4810e3f4856e05f2eeb0a6170e5e GIT 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+GGGAAAGTCAAGTGCGTAACTGCCGCACATGTCCTTACGGGCAATTCAGCTCGGGTTTCC +GGGGTCGGCTTCAATCAAATGCTTGACTTTGACGTAAAGGGAGATTTCGCTATAGCTGAT +TGCCCGAATTGGCAAGGGGCTGCCCCCAAGACCCAATTCTGCACGGATGGATGGACTGGC +CGTGCCTATTGGCTAACATCCTCTGGCGTCGAACCCGGCGTCATTGGAAAAGGATTCGCC +TTCTGCTTCACCGCATGTGGCGATTCCGGGTCCCCAGTGATCACCGAGGCCGGTGAGCTT +GTCGGCGTTCACACGGGATCGAATAAACAAGGGGGGGGCATTGTTACGCGCCCCTCAGGC +CAGTTTTGTAATGTGGCACCCATCAAGCTAAGCGAATTAAGTGAATTCTTTGCTGGGCCT +AAGGTCCCGCTCGGTGATGTGAAGGTCGGCAGCCACATAATTAAAGACATAAGCGAGGTG +CCTTCAGATCTTTGTGCCTTGCTTGCTGCCAAACCTGAACTGGAAGGAGGCCTCTCCACC +GTCCAACTTCTTTGTGTGTTTTTTCTCCTGTGGAGAATGATGGGACATGCCTGGACGCCC +TTGGTTGCTGTGAGTTTCTTTATTTTGAATGAGGTTCTCCCAGCCGTCCTGGTCCGGAGT +GTTTTCTCCTTTGGAATGTTTGTGCTATCCTGGCTCACGCCATGGTCTGCGCAAGTTCTG +ATGATCAGGCTTCTGACAGCAGCTCTTAACAGGAACAGATGGTCACTTGCCTTTTTCAGC +CTCGGTGCAGTGACCGGTTTTGTCGCAGATCTTGCGGCCACTCAGGGGCATCCGTTGCAG +GCAGTGATGAATTTGAGCACCTATGCATTCCTGCCTCGGATGATGGTTGTGACCTCACCA +GTCCCAGTGATCACGTGTGGTGTCGTGCACCTACTTGCCATCATTTTGTACTTGTTTAAG +TACCGTGGCCCGCACCATATCCTTGTTGGCGATGGAGTGTTCTCTGCGGCTTTCTTCTTG +AGATACTTTGCCGAG diff --git a/data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/sequences.fasta b/data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/sequences.fasta new file mode 100644 index 000000000..e04b2b6e8 --- /dev/null +++ b/data_output/community/UdeM-LMIVV/BabyV/PRRSV2/nsp3-4-5/Baby2026/unreleased/sequences.fasta @@ -0,0 +1,256 @@ +>MN046230.1 +GGAGGCCCACACCTCGCAGCTGCTCTGCATGTTGCCTGCTCGATGACCTTGCACATGCTT +GCTGGAATCTATGTGACCTCGGTGAGCACCTGCGGCACCGGCACCAATGACCCGTGGTGC +ACCAATCCGTTTGCCGTCCCTGGTTACGGACCCGGCTCTCTCTGCACGTCTAGGTTGTGC +ATCTCCCAGCATGGCCTTACACTGCCCTTGACGGCGTTGGTGGCCGGTTTCGGCATTCAG +GAAGTCGCTTTGGTTGTTTTAATCTTAATTTCCATCGGTGGCTTGGCTCACCGGTTGAGT +TGCAAGGCTGATGTGATGTTTGTTTTACTCGCAATCGCTTGCTATGTTTGGGAACCTCTC +ACCTGGTTGCTTTGTGTGTTTCCTTGCTGGCTGCGGTATTTTTCTTTGCACCCTTTCACT +ATTCTATGGTTAGTGTTTTTCTTGATCGCTGTAAACGCGCCTTCGGGGATCTTAGCCTTG +GTGTTGTTGGTCGTTCTTTGGCTCCTCGGCCGCTATACCAATGTTGCTGGTCTTGTCACC +CCCTATGACATCCACCATTACACCAATGGCCCCCGTGGTGTTGCTGCCTTGGCCACCGCA +CCGGAAGGAACCTACCTGGCCGCTGTCCGCCGCGCCGCGTTGACTGGTCGCACCATGCTG +TTCACCCCGTCTCAGCTTGGGTCCCTCCTTGAGGGTGCTTTCAGAACTCAAAAGCCCTCA +CTGAATACCGTCAATGTGGTCGGGTCCTCCATGGGCTCTGGCGGAGTGTTCAATATTGAC +GGGAAAATCAAGTGCGTGACTGCCGCACATGTCCTTACGGGTAACTCAGCTAGGGTTTCC +GGGGTCGGCTTTAATCAGATGCTTGACTTTGATGTAAAAGGGGACTTCGCCATAGCTGAT +TGCCCGAATTGGCAAGGAGTTGCTCCCAAGGCCCAGTTCTGTAAGGATGGGTGGACTGGC +CGCGCCTATTGGCTGACATCTTCTGGCGTTGAACCCGGTGTTATTGGGAATGGGTTCGCC +TTCTGCTTCACCGCGTGTGGTGATTCTGGATCCCCAGTGATTACCGAAGCCGGTGAGCTT +GTCGGCGTTCATACAGGGTCAAACAAACAAGGAGGAGGCATTGTCACGCGCCCCTCAGGC +CAGTTTTGTAATGTGAAGTCCATCAAGCTGAGCGAATTGAGTGAATTCTTCGCTGGACCC +AAGGTCCCGCTCGGTGATGTAAAACTCGGCAGTCACATAGTTAAAGACACACACGAGGTG +CCTTCAGATCTTTGTGCCCTGCTTGCTGCCAAACCTGAACTGGAAGGAGGTCTTTCCACA +GTTCAACTTCTGTGTGTGTTTTTCCTCCTGTGGAGGATGATGGGGCATGCCTGGACGCCT +TTGGTTGCTGTGGGGTTTTTCCTCCTGAATGAGATTCTCCCAGCTGTCCTGGTCCGGAGT +GCTTTCTCCTTCGGGATGTTTGTGCTGTCCTGGCTCACGCCATGGTCTGCGCAAGTCCTG +ATGATCAGGCTTCTGACAGCAGCCCTTAACAGAAACAAATTGTCTCTTGGTTTTTACAGC +CTTGGGGCAATAACCAGTTTTGTCGCAGACCTTGCGGTGACTCAAGGGCGCCCGTTACAG +GTGGTAATGAACCTGAGCACTTATGCCTTCTTGCCCCGAATGATGGTTGTGTCCTCACCA +GTCCCGGTGATCGCTTGCGGCGTCGTGCACCTCCTTGCCATAATTTTGTACTTGTTTAAG +TACCGCTGTCTTCATAATGTCCTTGTTGGCGATGGAGCATTCTCTTCGGCTTTTTTTTTG +CGATACTTTGCCGAG +>ON365556.1 +GGAGGCCCACACCTCATTGCTGCCTTGCATGTTGCTTGCTCGATGGCTCTTCACATGCTT +GCCGGGATTTATGTGACCTCGGTGAGCACCTGCGGCACTGGCACTAACGACCCGTGGTGT +ACCAATCCGTTTGCCGTCCCTGGTTACGGACCCGGCTCACTCTGCACGTCTAGGTTGTGT +ATCTCCCAGCATGGCCTCACACTACCCTTGACGGCGCTAGTGGCTGGGTTCGGTATTCAG +GAGATTGCTTTGGTTGTTTTAATCTTTGTTTCTATCGGTGGTTTGGCTCATCGGTTGAGT +TGCAAGGCTGACATGTTGTGCATCTTACTCGCAATCGCTAGTTATGTTTGGGAACCTCTC +ACTTGGTTGCTTTGTGTGTTTCCTTGTTGGCTGCGGTGTTTTCCTTTGCATCCTTTCACC +GTTCTATGGTTGGTGTTTTTCTTGATCTCTGTAAATGCGCCTTCGGGGATTTTGGCTGTG +GTGTTATTGGTTTCCCTCTGGCTTTTAGGTCGTTATACTAACATTGCTGGTCTTGTCACC 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