From bf9fd0e194252eb6a9b2d668521fbb3793640306 Mon Sep 17 00:00:00 2001 From: James Siqueira Date: Mon, 12 Aug 2024 14:51:42 -0300 Subject: [PATCH 01/26] dengue-lineages added --- .../dengue-lineages/all-serotypes/README.md | 10 + .../all-serotypes/denv1/CHANGELOG.md | 5 + .../all-serotypes/denv1/README.md | 27 + .../denv1/genome_annotation.gff3 | 15 + .../all-serotypes/denv1/pathogen.json | 74 + .../all-serotypes/denv1/reference.fasta | 156 + .../all-serotypes/denv1/tree.json | 44660 ++++++++++++ .../all-serotypes/denv2/CHANGELOG.md | 5 + .../all-serotypes/denv2/README.md | 28 + .../denv2/genome_annotation.gff3 | 15 + .../all-serotypes/denv2/pathogen.json | 74 + .../all-serotypes/denv2/reference.fasta | 156 + .../all-serotypes/denv2/tree.json | 58440 ++++++++++++++++ .../all-serotypes/denv3/CHANGELOG.md | 5 + .../all-serotypes/denv3/README.md | 27 + .../denv3/genome_annotation.gff3 | 15 + .../all-serotypes/denv3/pathogen.json | 74 + .../all-serotypes/denv3/reference.fasta | 155 + .../all-serotypes/denv3/tree.json | 23644 +++++++ .../all-serotypes/denv4/CHANGELOG.md | 5 + .../all-serotypes/denv4/README.md | 27 + .../denv4/genome_annotation.gff3 | 15 + .../all-serotypes/denv4/pathogen.json | 74 + .../all-serotypes/denv4/reference.fasta | 155 + .../all-serotypes/denv4/tree.json | 24439 +++++++ 25 files changed, 152300 insertions(+) create mode 100644 data/community/dengue-lineages/all-serotypes/README.md create mode 100644 data/community/dengue-lineages/all-serotypes/denv1/CHANGELOG.md create mode 100644 data/community/dengue-lineages/all-serotypes/denv1/README.md create mode 100644 data/community/dengue-lineages/all-serotypes/denv1/genome_annotation.gff3 create mode 100644 data/community/dengue-lineages/all-serotypes/denv1/pathogen.json create mode 100644 data/community/dengue-lineages/all-serotypes/denv1/reference.fasta create mode 100644 data/community/dengue-lineages/all-serotypes/denv1/tree.json create mode 100644 data/community/dengue-lineages/all-serotypes/denv2/CHANGELOG.md create mode 100644 data/community/dengue-lineages/all-serotypes/denv2/README.md create mode 100644 data/community/dengue-lineages/all-serotypes/denv2/genome_annotation.gff3 create mode 100644 data/community/dengue-lineages/all-serotypes/denv2/pathogen.json create mode 100644 data/community/dengue-lineages/all-serotypes/denv2/reference.fasta create mode 100644 data/community/dengue-lineages/all-serotypes/denv2/tree.json create mode 100644 data/community/dengue-lineages/all-serotypes/denv3/CHANGELOG.md create mode 100644 data/community/dengue-lineages/all-serotypes/denv3/README.md create mode 100644 data/community/dengue-lineages/all-serotypes/denv3/genome_annotation.gff3 create mode 100644 data/community/dengue-lineages/all-serotypes/denv3/pathogen.json create mode 100644 data/community/dengue-lineages/all-serotypes/denv3/reference.fasta create mode 100644 data/community/dengue-lineages/all-serotypes/denv3/tree.json create mode 100644 data/community/dengue-lineages/all-serotypes/denv4/CHANGELOG.md create mode 100644 data/community/dengue-lineages/all-serotypes/denv4/README.md create mode 100644 data/community/dengue-lineages/all-serotypes/denv4/genome_annotation.gff3 create mode 100644 data/community/dengue-lineages/all-serotypes/denv4/pathogen.json create mode 100644 data/community/dengue-lineages/all-serotypes/denv4/reference.fasta create mode 100644 data/community/dengue-lineages/all-serotypes/denv4/tree.json diff --git a/data/community/dengue-lineages/all-serotypes/README.md b/data/community/dengue-lineages/all-serotypes/README.md new file mode 100644 index 00000000..fcefc72e --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/README.md @@ -0,0 +1,10 @@ +# Implementation of the Dengue Lineages System for Designation via NextClade + +These datasets are based on the dengue virus lineage systems described by [Verity et al., 2024](https://doi.org/10.1101/2024.05.16.24307504), and are suitable for the analysis of viral sequences from the four dengue virus serotypes (DENV1 to DENV4). The systems are independent; therefore, each serotype should be analyzed in the corresponding specific dataset. + +More information about the Dengue Lineages project: [Dengue Lineages website](https://dengue-lineages.org/), [GitHub Repository](https://github.com/DENV-lineages) + + +## Authors and contacts + +Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri). \ No newline at end of file diff --git a/data/community/dengue-lineages/all-serotypes/denv1/CHANGELOG.md b/data/community/dengue-lineages/all-serotypes/denv1/CHANGELOG.md new file mode 100644 index 00000000..495dc86a --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv1/CHANGELOG.md @@ -0,0 +1,5 @@ +## Unreleased + +Initial release of a DENV-1 dataset for Lineage classification! + +Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data/community/dengue-lineages/all-serotypes/denv1/README.md b/data/community/dengue-lineages/all-serotypes/denv1/README.md new file mode 100644 index 00000000..a04465cc --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv1/README.md @@ -0,0 +1,27 @@ +# Nextclade dataset for "DENV-1 Lineages" based on reference "NC_001477.1" + + +## Dataset attributes + +| attribute | value | +| -------------------- | ---------------------------------------- | +| name | DENV-1 | +| refName | NC_001477 | +| refAccession | NC_001477.1 | + +## Scope of this Dataset +This dataset is based on the dengue virus lineage system from [Verity et al., 2024](https://doi.org/10.1101/2024.05.16.24307504) and is suitable for the analysis of DENV-1 viral sequences. The systems are independent, so sequences from other serotypes may not be classified or may be assigned as "Outgroup." + +## Authors and contacts + +Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri). + +## Dengue Lineages System Project + +This system is built off experience developing lineage systems for other viruses of public health importance, and is the result of a global collaboration of researchers and public health professionals. It aims to provide additional spatial and temporal resolution with which to discuss the large genetic diversity of dengue virus. Specifically, it splits up existing genotypes into smaller groups and provides a standardized, neutral naming system. + +Broadly speaking, we define major and minor lineages within each genotype. These lineages are defined by the same rules, but use different nomenclature. In theory, minor lineages should be more useful for country-specific questions, and major lineages for regional questions. Of course, it won't always necessarily work like that - some minor lineages are very widespread, and some major lineages are geographically limited. + +## 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/dengue-lineages/all-serotypes/denv1/genome_annotation.gff3 b/data/community/dengue-lineages/all-serotypes/denv1/genome_annotation.gff3 new file mode 100644 index 00000000..a620c819 --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv1/genome_annotation.gff3 @@ -0,0 +1,15 @@ +##gff-version 3 +##source-version geneious 2022.2.2 +##sequence-region NC_001477.1 1 10735 +NC_001477.1 Geneious gene 95 436 . + . gene_name=C +NC_001477.1 Geneious gene 437 934 . + . gene_name=M +NC_001477.1 Geneious gene 437 709 . + . gene_name=pr +NC_001477.1 Geneious gene 935 2419 . + . gene_name=E +NC_001477.1 Geneious gene 2420 3475 . + . gene_name=NS1 +NC_001477.1 Geneious gene 3476 4129 . + . gene_name=NS2A +NC_001477.1 Geneious gene 4130 4519 . + . gene_name=NS2B +NC_001477.1 Geneious gene 4520 6376 . + . gene_name=NS3 +NC_001477.1 Geneious gene 6377 6757 . + . gene_name=NS4A +NC_001477.1 Geneious gene 6758 6826 . + . gene_name=2K +NC_001477.1 Geneious gene 6827 7573 . + . gene_name=NS4B +NC_001477.1 Geneious gene 7574 10270 . + . gene_name=NS5 diff --git a/data/community/dengue-lineages/all-serotypes/denv1/pathogen.json b/data/community/dengue-lineages/all-serotypes/denv1/pathogen.json new file mode 100644 index 00000000..560eb3f7 --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv1/pathogen.json @@ -0,0 +1,74 @@ +{ + "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", + "minSeedCover": 0.1, + "minLength": 1000 + }, + "attributes": { + "name": "DENV-1 lineages", + "reference accession": "NC_001477.1", + "reference name": "NC_001477" + }, + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + }, + "placementMaskRanges":[ + {"begin":0, "end":94}, + {"begin":10271, "end":10735} + ], + "deprecated": false, + "enabled": true, + "experimental": true, + "files": { + "changelog": "CHANGELOG.md", + "genomeAnnotation": "genome_annotation.gff3", + "pathogenJson": "pathogen.json", + "readme": "README.md", + "reference": "reference.fasta", + "treeJson": "tree.json" + }, + "meta": { + "bugs": "https://github.com/DENV-lineages/nextclade_data/issues", + "source code": "https://github.com/DENV-lineages/nextclade_data" + }, + "qc": { + "frameShifts": { + "enabled": true + }, + "missingData": { + "enabled": true, + "missingDataThreshold": 1000, + "scoreBias": 100 + }, + "mixedSites": { + "enabled": false, + "mixedSitesThreshold": 8 + }, + "privateMutations": { + "cutoff": 25, + "enabled": true, + "typical": 10, + "weightLabeledSubstitutions": 2, + "weightReversionSubstitutions": 1, + "weightUnlabeledSubstitutions": 1 + }, + "snpClusters": { + "clusterCutOff": 5, + "enabled": false, + "scoreWeight": 50, + "windowSize": 100 + }, + "stopCodons": { + "enabled": true + } + }, + "schemaVersion": "3.0.0", + "version": { + "tag": "unreleased" + }, + "defaultCds": "E" +} diff --git a/data/community/dengue-lineages/all-serotypes/denv1/reference.fasta b/data/community/dengue-lineages/all-serotypes/denv1/reference.fasta new file mode 100644 index 00000000..4f24c8f4 --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv1/reference.fasta @@ -0,0 +1,156 @@ +>NC_001477.1 Dengue virus 1, complete genome +AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGAATCGGAAGCTTGCTTAACGTAGTTCTAACAGT +TTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAAAAGACGGGTCGACCGTCTTTCAATATGC +TGAAACGCGCGAGAAACCGCGTGTCAACTGTTTCACAGTTGGCGAAGAGATTCTCAAAAGGATTGCTTTC +AGGCCAAGGACCCATGAAATTGGTGATGGCTTTTATAGCATTCCTAAGATTTCTAGCCATACCTCCAACA +GCAGGAATTTTGGCTAGATGGGGCTCATTCAAGAAGAATGGAGCGATCAAAGTGTTACGGGGTTTCAAGA 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a/data/community/dengue-lineages/all-serotypes/denv2/CHANGELOG.md b/data/community/dengue-lineages/all-serotypes/denv2/CHANGELOG.md new file mode 100644 index 00000000..2be82eea --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv2/CHANGELOG.md @@ -0,0 +1,5 @@ +## Unreleased + +Initial release of a DENV-2 dataset for Lineage classification! + +Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data/community/dengue-lineages/all-serotypes/denv2/README.md b/data/community/dengue-lineages/all-serotypes/denv2/README.md new file mode 100644 index 00000000..1c005418 --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv2/README.md @@ -0,0 +1,28 @@ +# Nextclade dataset for "denv-2" based on reference "NC_001474" + + +## Dataset attributes + +| attribute | value | +| -------------------- | ---------------------------------------- | +| name | denv-2 | +| refName | NC_001474 | +| refAccession | NC_001474.2 | + +## Scope of this Dataset +This dataset is based on the dengue virus lineage system from [Verity et al., 2024](https://doi.org/10.1101/2024.05.16.24307504) and is suitable for the analysis of DENV-2 viral sequences. The systems are independent, so sequences from other serotypes may not be classified or may be assigned as "Outgroup." + +## Authors and contacts + +Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri). + +## Dengue Lineages System Project + +This system is built off experience developing lineage systems for other viruses of public health importance, and is the result of a global collaboration of researchers and public health professionals. It aims to provide additional spatial and temporal resolution with which to discuss the large genetic diversity of dengue virus. Specifically, it splits up existing genotypes into smaller groups and provides a standardized, neutral naming system. + +Broadly speaking, we define major and minor lineages within each genotype. These lineages are defined by the same rules, but use different nomenclature. In theory, minor lineages should be more useful for country-specific questions, and major lineages for regional questions. Of course, it won't always necessarily work like that - some minor lineages are very widespread, and some major lineages are geographically limited. + + +## 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/dengue-lineages/all-serotypes/denv2/genome_annotation.gff3 b/data/community/dengue-lineages/all-serotypes/denv2/genome_annotation.gff3 new file mode 100644 index 00000000..4c4270f3 --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv2/genome_annotation.gff3 @@ -0,0 +1,15 @@ +##gff-version 3 +##source-version geneious 2022.2.2 +##sequence-region NC_001474.2 1 10723 +NC_001474.2 Geneious gene 97 438 . + . gene_name=C +NC_001474.2 Geneious gene 439 936 . + . gene_name=M +NC_001474.2 Geneious gene 439 711 . + . gene_name=pr +NC_001474.2 Geneious gene 937 2421 . + . gene_name=E +NC_001474.2 Geneious gene 2422 3477 . + . gene_name=NS1 +NC_001474.2 Geneious gene 3478 4131 . + . gene_name=NS2A +NC_001474.2 Geneious gene 4132 4521 . + . gene_name=NS2B +NC_001474.2 Geneious gene 4522 6375 . + . gene_name=NS3 +NC_001474.2 Geneious gene 6376 6756 . + . gene_name=NS4A +NC_001474.2 Geneious gene 6757 6825 . + . gene_name=2K +NC_001474.2 Geneious gene 6826 7569 . + . gene_name=NS4B +NC_001474.2 Geneious gene 7570 10269 . + . gene_name=NS5 diff --git a/data/community/dengue-lineages/all-serotypes/denv2/pathogen.json b/data/community/dengue-lineages/all-serotypes/denv2/pathogen.json new file mode 100644 index 00000000..4e5f5cfc --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv2/pathogen.json @@ -0,0 +1,74 @@ +{ + "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", + "minSeedCover": 0.1, + "minLength": 1000 + }, + "attributes": { + "name": "DENV-2 lineages", + "reference accession": "NC_001474.2", + "reference name": "NC_001474" + }, + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + }, + "placementMaskRanges":[ + {"begin":0, "end":94}, + {"begin":10271, "end":10735} + ], + "deprecated": false, + "enabled": true, + "experimental": true, + "files": { + "changelog": "CHANGELOG.md", + "genomeAnnotation": "genome_annotation.gff3", + "pathogenJson": "pathogen.json", + "readme": "README.md", + "reference": "reference.fasta", + "treeJson": "tree.json" + }, + "meta": { + "bugs": "https://github.com/DENV-lineages/nextclade_data/issues", + "source code": "https://github.com/DENV-lineages/nextclade_data" + }, + "qc": { + "frameShifts": { + "enabled": true + }, + "missingData": { + "enabled": true, + "missingDataThreshold": 1000, + "scoreBias": 100 + }, + "mixedSites": { + "enabled": false, + "mixedSitesThreshold": 8 + }, + "privateMutations": { + "cutoff": 25, + "enabled": true, + "typical": 10, + "weightLabeledSubstitutions": 2, + "weightReversionSubstitutions": 1, + "weightUnlabeledSubstitutions": 1 + }, + "snpClusters": { + "clusterCutOff": 5, + "enabled": false, + "scoreWeight": 50, + "windowSize": 100 + }, + "stopCodons": { + "enabled": true + } + }, + "schemaVersion": "3.0.0", + "version": { + "tag": "unreleased" + }, + "defaultCds": "E" +} diff --git a/data/community/dengue-lineages/all-serotypes/denv2/reference.fasta b/data/community/dengue-lineages/all-serotypes/denv2/reference.fasta new file mode 100644 index 00000000..66d11c6b --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv2/reference.fasta @@ -0,0 +1,156 @@ +>NC_001474.2 Dengue virus 2, complete genome +AGTTGTTAGTCTACGTGGACCGACAAAGACAGATTCTTTGAGGGAGCTAAGCTCAACGTAGTTCTAACAG +TTTTTTAATTAGAGAGCAGATCTCTGATGAATAACCAACGGAAAAAGGCGAAAAACACGCCTTTCAATAT +GCTGAAACGCGAGAGAAACCGCGTGTCGACTGTGCAACAGCTGACAAAGAGATTCTCACTTGGAATGCTG +CAGGGACGAGGACCATTAAAACTGTTCATGGCCCTGGTGGCGTTCCTTCGTTTCCTAACAATCCCACCAA +CAGCAGGGATATTGAAGAGATGGGGAACAATTAAAAAATCAAAAGCTATTAATGTTTTGAGAGGGTTCAG 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+++ b/data/community/dengue-lineages/all-serotypes/denv3/README.md @@ -0,0 +1,27 @@ +# Nextclade dataset for "DENV-3 Lineages" based on reference "NC_001475" + + +## Dataset attributes + +| attribute | value | +| -------------------- | ---------------------------------------- | +| name | DENV-3 | +| refName | NC_001475 | +| refAccession | NC_001475.2 | + +## Scope of this Dataset +This dataset is based on the dengue virus lineage system from [Verity et al., 2024](https://doi.org/10.1101/2024.05.16.24307504) and is suitable for the analysis of DENV-3 viral sequences. The systems are independent, so sequences from other serotypes may not be classified or may be assigned as "Outgroup." + +## Authors and contacts + +Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri). + +## Dengue Lineages System Project + +This system is built off experience developing lineage systems for other viruses of public health importance, and is the result of a global collaboration of researchers and public health professionals. It aims to provide additional spatial and temporal resolution with which to discuss the large genetic diversity of dengue virus. Specifically, it splits up existing genotypes into smaller groups and provides a standardized, neutral naming system. + +Broadly speaking, we define major and minor lineages within each genotype. These lineages are defined by the same rules, but use different nomenclature. In theory, minor lineages should be more useful for country-specific questions, and major lineages for regional questions. Of course, it won't always necessarily work like that - some minor lineages are very widespread, and some major lineages are geographically limited. + +## 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/dengue-lineages/all-serotypes/denv3/genome_annotation.gff3 b/data/community/dengue-lineages/all-serotypes/denv3/genome_annotation.gff3 new file mode 100644 index 00000000..85320dbf --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv3/genome_annotation.gff3 @@ -0,0 +1,15 @@ +##gff-version 3 +##source-version geneious 2022.2.2 +##sequence-region NC_001475 1 10707 +NC_001475 Geneious gene 95 436 . + . gene_name=C +NC_001475 Geneious gene 437 934 . + . gene_name=M +NC_001475 Geneious gene 437 709 . + . gene_name=pr +NC_001475 Geneious gene 935 2413 . + . gene_name=E +NC_001475 Geneious gene 2414 3469 . + . gene_name=NS1 +NC_001475 Geneious gene 3470 4123 . + . gene_name=NS2A +NC_001475 Geneious gene 4124 4513 . + . gene_name=NS2B +NC_001475 Geneious gene 4514 6370 . + . gene_name=NS3 +NC_001475 Geneious gene 6371 6751 . + . gene_name=NS4A +NC_001475 Geneious gene 6752 6820 . + . gene_name=2K +NC_001475 Geneious gene 6821 7564 . + . gene_name=NS4B +NC_001475 Geneious gene 7565 10264 . + . gene_name=NS5 diff --git a/data/community/dengue-lineages/all-serotypes/denv3/pathogen.json b/data/community/dengue-lineages/all-serotypes/denv3/pathogen.json new file mode 100644 index 00000000..a04d95b6 --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv3/pathogen.json @@ -0,0 +1,74 @@ +{ + "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", + "minSeedCover": 0.1, + "minLength": 1000 + }, + "attributes": { + "name": "DENV-3 lineages", + "reference accession": "NC_001475.2", + "reference name": "NC_001475" + }, + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + }, + "placementMaskRanges":[ + {"begin":0, "end":94}, + {"begin":10268, "end":10707} + ], + "deprecated": false, + "enabled": true, + "experimental": true, + "files": { + "changelog": "CHANGELOG.md", + "genomeAnnotation": "genome_annotation.gff3", + "pathogenJson": "pathogen.json", + "readme": "README.md", + "reference": "reference.fasta", + "treeJson": "tree.json" + }, + "meta": { + "bugs": "https://github.com/DENV-lineages/nextclade_data/issues", + "source code": "https://github.com/DENV-lineages/nextclade_data" + }, + "qc": { + "frameShifts": { + "enabled": true + }, + "missingData": { + "enabled": true, + "missingDataThreshold": 1000, + "scoreBias": 100 + }, + "mixedSites": { + "enabled": false, + "mixedSitesThreshold": 8 + }, + "privateMutations": { + "cutoff": 25, + "enabled": true, + "typical": 10, + "weightLabeledSubstitutions": 2, + "weightReversionSubstitutions": 1, + "weightUnlabeledSubstitutions": 1 + }, + "snpClusters": { + "clusterCutOff": 5, + "enabled": false, + "scoreWeight": 50, + "windowSize": 100 + }, + "stopCodons": { + "enabled": true + } + }, + "schemaVersion": "3.0.0", + "version": { + "tag": "unreleased" + }, + "defaultCds": "E" +} diff --git a/data/community/dengue-lineages/all-serotypes/denv3/reference.fasta b/data/community/dengue-lineages/all-serotypes/denv3/reference.fasta new file mode 100644 index 00000000..8baa3e03 --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv3/reference.fasta @@ -0,0 +1,155 @@ +>NC_001475.2 Dengue virus 3, complete genome +AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGACTCGGAAGCTTGCTTAACGTAGTGCTGACAGT +TTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAGAAGACGGGAAAACCGTCTATCAATATGC +TGAAACGCGTGAGAAACCGTGTGTCAACTGGATCACAGTTGGCGAAGAGATTCTCAAAAGGACTGCTGAA +CGGCCAGGGACCAATGAAATTGGTTATGGCGTTCATAGCTTTCCTCAGATTTCTAGCCATTCCACCAACA +GCAGGAGTCTTGGCTAGATGGGGAACCTTCAAGAAGTCGGGGGCCATTAAGGTCCTGAAAGGCTTCAAGA 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"/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 95, + "strand": "+", + "type": "CDS" + }, + "E": { + "end": 2413, + "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 935, + "strand": "+", + "type": "CDS" + }, + "M": { + "end": 934, + "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 437, + "strand": "+", + "type": "CDS" + }, + "NS1": { + "end": 3469, + "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 2414, + "strand": "+", + "type": "CDS" + }, + "NS2A": { + "end": 4123, + "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 3470, + "strand": "+", + "type": "CDS" + }, + "NS2B": { + "end": 4513, + "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 4124, + "strand": "+", + "type": "CDS" + }, + "NS3": { + "end": 6370, + "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 4514, + "strand": "+", + "type": "CDS" + }, + "NS4A": { + "end": 6751, + "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 6371, + "strand": "+", + "type": "CDS" + }, + "NS4B": { + "end": 7564, + "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 6821, + "strand": "+", + "type": "CDS" + }, + "NS5": { + "end": 10264, + "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 7565, + "strand": "+", + "type": "CDS" + }, + "nuc": { + "end": 10707, + "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 1, + "strand": "+", + "type": "source" + }, + "pr": { + "end": 709, + "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", + "start": 437, + "strand": "+", + "type": "CDS" + } + }, + "colorings": [ + { + "key": "clade_membership", + "title": "Lineage", + "type": "categorical" + }, + { + "key": "gt", + "title": "Genotype", + "type": "categorical" + } + ], + "filters": [ + "clade_membership" + ], + "panels": [ + "tree", + "entropy" + ] + }, + "tree": { + "name": "NODE_0000000", + "node_attrs": { + "div": 0, + "clade_membership": { + "value": "unassigned" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G112A", + "A198G", + "C203T", + "G217A", + "T235A", + "A277G", + "C310T", + "C325T", + "G337A", + "A376T", + "C383A", + "A418G", + "G421A", + "G428A", + "T496A", + "A616G", + "T646G", + "A652G", + 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"G2017A", + "G2203A" + ] + } + }, + "children": [ + { + "name": "OQ857506.1|2022-10-05", + "node_attrs": { + "div": 0.10508479, + "clade_membership": { + "value": "3III_B.3.2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G451A", + "A1321G", + "T2056C", + "C3013T", + "A3643G", + "T4025A", + "C4339T", + "A4888G", + "C7193T", + "G7267A", + "A7891G", + "A8406G" + ], + "NS2A": [ + "I58M", + "L186M" + ], + "NS5": [ + "K281R" + ] + }, + "labels": { + "aa": "NS2A: I58M, L186M; NS5: K281R" + } + } + }, + { + "name": "OR150747.1|2022-12-23", + "node_attrs": { + "div": 0.10501596, + "clade_membership": { + "value": "3III_B.3.2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T1159C", + "T1825C", + "T2171C", + "C2314T", + "T2491C", + "A2734G", + "T4744C", + "G5173A", + "T5494A", + "T5671C", + "C6754T", + "C6857T", + "A9772G", + "C9841T", + "C10079T", + "G10243T" + ], + "NS5": [ + "E893D" + ] + }, + "labels": { + "aa": "NS5: E893D" + } + } + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } +} diff --git a/data/community/dengue-lineages/all-serotypes/denv4/CHANGELOG.md b/data/community/dengue-lineages/all-serotypes/denv4/CHANGELOG.md new file mode 100644 index 00000000..39445c0f --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv4/CHANGELOG.md @@ -0,0 +1,5 @@ +## Unreleased + +Initial release of a DENV-4 dataset for Lineage classification! + +Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data/community/dengue-lineages/all-serotypes/denv4/README.md b/data/community/dengue-lineages/all-serotypes/denv4/README.md new file mode 100644 index 00000000..961d30b6 --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv4/README.md @@ -0,0 +1,27 @@ +# Nextclade dataset for "DENV-4 Lineages" based on reference "NC_002640" + + +## Dataset attributes + +| attribute | value | +| -------------------- | ---------------------------------------- | +| name | DENV-4 | +| refName | NC_002640 | +| refAccession | NC_002640.1 | + +## Scope of this Dataset +This dataset is based on the dengue virus lineage system from [Verity et al., 2024](https://doi.org/10.1101/2024.05.16.24307504) and is suitable for the analysis of DENV-4 viral sequences. The systems are independent, so sequences from other serotypes may not be classified or may be assigned as "Outgroup." + +## Authors and contacts + +Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri). + +## Dengue Lineages System Project + +This system is built off experience developing lineage systems for other viruses of public health importance, and is the result of a global collaboration of researchers and public health professionals. It aims to provide additional spatial and temporal resolution with which to discuss the large genetic diversity of dengue virus. Specifically, it splits up existing genotypes into smaller groups and provides a standardized, neutral naming system. + +Broadly speaking, we define major and minor lineages within each genotype. These lineages are defined by the same rules, but use different nomenclature. In theory, minor lineages should be more useful for country-specific questions, and major lineages for regional questions. Of course, it won't always necessarily work like that - some minor lineages are very widespread, and some major lineages are geographically limited. + +## 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/dengue-lineages/all-serotypes/denv4/genome_annotation.gff3 b/data/community/dengue-lineages/all-serotypes/denv4/genome_annotation.gff3 new file mode 100644 index 00000000..dee12411 --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv4/genome_annotation.gff3 @@ -0,0 +1,15 @@ +##gff-version 3 +##source-version geneious 2022.2.2 +##sequence-region NC_002640 1 10649 +NC_002640 Geneious gene 102 440 . + . gene_name=C +NC_002640 Geneious gene 441 938 . + . gene_name=M +NC_002640 Geneious gene 441 713 . + . gene_name=pr +NC_002640 Geneious gene 939 2423 . + . gene_name=E +NC_002640 Geneious gene 2424 3479 . + . gene_name=NS1 +NC_002640 Geneious gene 3480 4133 . + . gene_name=NS2A +NC_002640 Geneious gene 4134 4523 . + . gene_name=NS2B +NC_002640 Geneious gene 4524 6377 . + . gene_name=NS3 +NC_002640 Geneious gene 6378 6758 . + . gene_name=NS4A +NC_002640 Geneious gene 6759 6827 . + . gene_name=2K +NC_002640 Geneious gene 6828 7562 . + . gene_name=NS4B +NC_002640 Geneious gene 7563 10262 . + . gene_name=NS5 diff --git a/data/community/dengue-lineages/all-serotypes/denv4/pathogen.json b/data/community/dengue-lineages/all-serotypes/denv4/pathogen.json new file mode 100644 index 00000000..4847c303 --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv4/pathogen.json @@ -0,0 +1,74 @@ +{ + "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", + "minSeedCover": 0.1, + "minLength": 1000 + }, + "attributes": { + "name": "DENV-4 lineages", + "reference accession": "NC_002640.1", + "reference name": "NC_002640" + }, + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + }, + "placementMaskRanges":[ + {"begin":0, "end":101}, + {"begin":10266, "end":10649} + ], + "deprecated": false, + "enabled": true, + "experimental": true, + "files": { + "changelog": "CHANGELOG.md", + "genomeAnnotation": "genome_annotation.gff3", + "pathogenJson": "pathogen.json", + "readme": "README.md", + "reference": "reference.fasta", + "treeJson": "tree.json" + }, + "meta": { + "bugs": "https://github.com/DENV-lineages/nextclade_data/issues", + "source code": "https://github.com/DENV-lineages/nextclade_data" + }, + "qc": { + "frameShifts": { + "enabled": true + }, + "missingData": { + "enabled": true, + "missingDataThreshold": 1000, + "scoreBias": 100 + }, + "mixedSites": { + "enabled": false, + "mixedSitesThreshold": 8 + }, + "privateMutations": { + "cutoff": 25, + "enabled": true, + "typical": 10, + "weightLabeledSubstitutions": 2, + "weightReversionSubstitutions": 1, + "weightUnlabeledSubstitutions": 1 + }, + "snpClusters": { + "clusterCutOff": 5, + "enabled": false, + "scoreWeight": 50, + "windowSize": 100 + }, + "stopCodons": { + "enabled": true + } + }, + "schemaVersion": "3.0.0", + "version": { + "tag": "unreleased" + }, + "defaultCds": "E" +} diff --git a/data/community/dengue-lineages/all-serotypes/denv4/reference.fasta b/data/community/dengue-lineages/all-serotypes/denv4/reference.fasta new file mode 100644 index 00000000..3d10eace --- /dev/null +++ b/data/community/dengue-lineages/all-serotypes/denv4/reference.fasta @@ -0,0 +1,155 @@ +>NC_002640.1 Dengue virus 4, complete genome +AGTTGTTAGTCTGTGTGGACCGACAAGGACAGTTCCAAATCGGAAGCTTGCTTAACACAGTTCTAACAGT +TTGTTTGAATAGAGAGCAGATCTCTGGAAAAATGAACCAACGAAAAAAGGTGGTTAGACCACCTTTCAAT +ATGCTGAAACGCGAGAGAAACCGCGTATCAACCCCTCAAGGGTTGGTGAAGAGATTCTCAACCGGACTTT +TTTCTGGGAAAGGACCCTTACGGATGGTGCTAGCATTCATCACGTTTTTGCGAGTCCTTTCCATCCCACC +AACAGCAGGGATTCTGAAGAGATGGGGACAGTTGAAGAAAAATAAGGCCATCAAGATACTGATTGGATTC +AGGAAGGAGATAGGCCGCATGCTGAACATCTTGAACGGGAGAAAAAGGTCAACGATAACATTGCTGTGCT +TGATTCCCACCGTAATGGCGTTTTCCCTCAGCACAAGAGATGGCGAACCCCTCATGATAGTGGCAAAACA +TGAAAGGGGGAGACCTCTCTTGTTTAAGACAACAGAGGGGATCAACAAATGCACTCTCATTGCCATGGAC +TTGGGTGAAATGTGTGAGGACACTGTCACGTATAAATGCCCCCTACTGGTCAATACCGAACCTGAAGACA +TTGATTGCTGGTGCAACCTCACGTCTACCTGGGTCATGTATGGGACATGCACCCAGAGCGGAGAACGGAG +ACGAGAGAAGCGCTCAGTAGCTTTAACACCACATTCAGGAATGGGATTGGAAACAAGAGCTGAGACATGG +ATGTCATCGGAAGGGGCTTGGAAGCATGCTCAGAGAGTAGAGAGCTGGATACTCAGAAACCCAGGATTCG +CGCTCTTGGCAGGATTTATGGCTTATATGATTGGGCAAACAGGAATCCAGCGAACTGTCTTCTTTGTCCT +AATGATGCTGGTCGCCCCATCCTACGGAATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGA +GTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAA +AACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCAT +TGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAG +GAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGT +TTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCA +AATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGAC +ACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACT +ATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAAT +GAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCA +GACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGAC +AGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGA +CTCCGGTGATGGAAATCACATGTTTGCAGGACATCTTAAGTGCAAAGTCCGTATGGAGAAATTGAGAATC +AAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATG +GGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGA +TGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTA +ACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAA +CACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACG +AATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAG +GCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCC +TAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCGAGGAACACTTCAATGGCTATGACGTGCATAGC +TGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCAGACATGGGTTGTGTGGCGTCATGGAGT +GGGAAAGAATTGAAGTGTGGAAGCGGAATTTTTGTGGTTGACAACGTGCACACTTGGACAGAACAGTACA +AATTTCAACCAGAGTCCCCAGCGAGACTAGCGTCTGCAATATTAAATGCCCACAAAGATGGGGTCTGTGG +AATTAGATCAACCACGAGGCTGGAAAATGTCATGTGGAAGCAAATAACCAACGAGCTAAACTATGTTCTC +TGGGAAGGAGGACATGACCTCACTGTAGTGGCTGGGGATGTGAAGGGGGTGTTGACCAAAGGCAAGAGAG +CACTCACACCCCCAGTGAGTGATCTGAAATATTCATGGAAGACATGGGGAAAAGCAAAAATCTTCACCCC +AGAAGCAAGAAATAGCACATTTTTAATAGACGGACCAGACACCTCTGAATGCCCCAATGAACGAAGAGCA +TGGAACTCTCTTGAGGTGGAAGACTATGGATTTGGCATGTTCACGACCAACATATGGATGAAATTCCGAG +AAGGAAGTTCAGAAGTGTGTGACCACAGGTTAATGTCAGCTGCAATTAAAGATCAGAAAGCTGTGCATGC +TGACATGGGTTATTGGATAGAGAGCTCAAAAAACCAGACCTGGCAGATAGAGAAAGCATCTCTTATTGAA +GTGAAAACATGTCTGTGGCCCAAGACCCACACACTGTGGAGCAATGGAGTGCTGGAAAGCCAGATGCTCA +TTCCAAAATCATATGCGGGCCCTTTTTCACAGCACAATTACCGCCAGGGCTATGCCACGCAAACCGTGGG +CCCATGGCACTTAGGCAAATTAGAGATAGACTTTGGAGAATGCCCCGGAACAACAGTCACAATTCAGGAG +GATTGTGACCATAGAGGCCCATCTTTGAGGACCACCACTGCATCTGGAAAACTAGTCACGCAATGGTGCT +GCCGCTCCTGCACGATGCCTCCCTTAAGGTTCTTGGGAGAAGATGGGTGCTGGTATGGGATGGAGATTAG +GCCCTTGAGTGAAAAAGAAGAGAACATGGTCAAATCACAGGTGACGGCCGGACAGGGCACATCAGAAACT +TTTTCTATGGGTCTGTTGTGCCTGACCTTGTTTGTGGAAGAATGCTTGAGGAGAAGAGTCACTAGGAAAC +ACATGATATTAGTTGTGGTGATCACTCTTTGTGCTATCATCCTGGGAGGCCTCACATGGATGGACTTACT +ACGAGCCCTCATCATGTTGGGGGACACTATGTCTGGTAGAATAGGAGGACAGATCCACCTAGCCATCATG +GCAGTGTTCAAGATGTCACCAGGATACGTGCTGGGTGTGTTTTTAAGGAAACTCACTTCAAGAGAGACAG +CACTAATGGTAATAGGAATGGCCATGACAACGGTGCTTTCAATTCCACATGACCTTATGGAACTCATTGA +TGGAATATCACTGGGACTAATTTTGCTAAAAATAGTAACACAGTTTGACAACACCCAAGTGGGAACCTTA +GCTCTTTCCTTGACTTTCATAAGATCAACAATGCCATTGGTCATGGCTTGGAGGACCATTATGGCTGTGT 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+AACATTAGATTTCAAACCCGGAACGTCTGGTTCTCCCATCATCAACAGGAAAGGAAAAGTCATCGGACTC +TATGGAAATGGAGTAGTTACCAAATCAGGTGATTACGTCAGTGCCATAACGCAAGCCGAAAGAATTGGAG +AGCCAGATTATGAAGTGGATGAGGACATTTTTCGAAAGAAAAGATTAACTATAATGGACTTACACCCCGG +AGCTGGAAAGACAAAAAGAATTCTTCCATCAATAGTGAGAGAAGCCTTAAAAAGGAGGCTACGAACTTTG +ATTTTAGCTCCCACGAGAGTGGTGGCGGCCGAGATGGAAGAGGCCCTACGTGGACTGCCAATCCGTTATC +AGACCCCAGCTGTGAAATCAGAACACACAGGAAGAGAGATTGTAGACCTCATGTGTCATGCAACCTTCAC +AACAAGACTTTTGTCATCAACCAGGGTTCCAAATTACAACCTTATAGTGATGGATGAAGCACATTTCACC +GATCCTTCTAGTGTCGCGGCTAGAGGATACATCTCGACCAGGGTGGAAATGGGAGAGGCAGCAGCCATCT +TCATGACCGCAACCCCTCCCGGAGCGACAGATCCCTTTCCCCAGAGCAACAGCCCAATAGAAGACATCGA +GAGGGAAATTCCGGAAAGGTCATGGAACACAGGGTTCGACTGGATAACAGACTACCAAGGGAAAACTGTG +TGGTTTGTTCCCAGCATAAAAGCTGGAAATGACATTGCAAATTGTTTGAGAAAGTCGGGAAAGAAAGTTA +TCCAGTTGAGTAGGAAAACCTTTGATACAGAGTATCCAAAAACGAAACTCACGGACTGGGACTTTGTGGT +CACTACAGACATATCTGAAATGGGGGCCAATTTTAGAGCCGGGAGAGTGATAGACCCTAGAAGATGCCTC 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"name": "OQ427047.1|2019-01-15", + "node_attrs": { + "div": 0.2933574799999999, + "clade_membership": { + "value": "4I_A.1.2" + } + }, + "branch_attrs": { + "mutations": {} + } + }, + { + "name": "OQ427046.1|2019-01-15", + "node_attrs": { + "div": 0.2933574799999999, + "clade_membership": { + "value": "4I_A.1.2" + } + }, + "branch_attrs": { + "mutations": {} + } + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } +} From e009a93656178a3cd67005e8e624e2f7317c9f22 Mon Sep 17 00:00:00 2001 From: James Siqueira Date: Tue, 13 Aug 2024 06:49:35 -0300 Subject: [PATCH 02/26] Add example sequences --- .../dengue-lineages/all-serotypes/README.md | 0 .../all-serotypes/denv1/CHANGELOG.md | 0 .../all-serotypes/denv1/README.md | 0 .../denv1/genome_annotation.gff3 | 0 .../all-serotypes/denv1/pathogen.json | 3 +- .../all-serotypes/denv1/reference.fasta | 0 .../all-serotypes/denv1/sequences.fasta | 7964 +++++++++++ .../all-serotypes/denv1/tree.json | 0 .../all-serotypes/denv2/CHANGELOG.md | 0 .../all-serotypes/denv2/README.md | 0 .../denv2/genome_annotation.gff3 | 0 .../all-serotypes/denv2/pathogen.json | 3 +- .../all-serotypes/denv2/reference.fasta | 0 .../all-serotypes/denv2/sequences.fasta | 11640 ++++++++++++++++ .../all-serotypes/denv2/tree.json | 0 .../all-serotypes/denv3/CHANGELOG.md | 0 .../all-serotypes/denv3/README.md | 0 .../denv3/genome_annotation.gff3 | 0 .../all-serotypes/denv3/pathogen.json | 3 +- .../all-serotypes/denv3/reference.fasta | 0 .../all-serotypes/denv3/sequences.fasta | 4320 ++++++ .../all-serotypes/denv3/tree.json | 0 .../all-serotypes/denv4/CHANGELOG.md | 0 .../all-serotypes/denv4/README.md | 0 .../denv4/genome_annotation.gff3 | 0 .../all-serotypes/denv4/pathogen.json | 3 +- .../all-serotypes/denv4/reference.fasta | 0 .../all-serotypes/denv4/sequences.fasta | 3179 +++++ .../all-serotypes/denv4/tree.json | 0 29 files changed, 27111 insertions(+), 4 deletions(-) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/README.md (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv1/CHANGELOG.md (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv1/README.md (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv1/genome_annotation.gff3 (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv1/pathogen.json (96%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv1/reference.fasta (100%) create mode 100755 data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/sequences.fasta rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv1/tree.json (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv2/CHANGELOG.md (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv2/README.md (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv2/genome_annotation.gff3 (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv2/pathogen.json (96%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv2/reference.fasta (100%) create mode 100755 data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/sequences.fasta rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv2/tree.json (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv3/CHANGELOG.md (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv3/README.md (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv3/genome_annotation.gff3 (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv3/pathogen.json (96%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv3/reference.fasta (100%) create mode 100755 data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/sequences.fasta rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv3/tree.json (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv4/CHANGELOG.md (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv4/README.md (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv4/genome_annotation.gff3 (100%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv4/pathogen.json (96%) rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv4/reference.fasta (100%) create mode 100755 data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/sequences.fasta rename data/community/{ => v-gen-lab}/dengue-lineages/all-serotypes/denv4/tree.json (100%) diff --git a/data/community/dengue-lineages/all-serotypes/README.md b/data/community/v-gen-lab/dengue-lineages/all-serotypes/README.md similarity index 100% rename from data/community/dengue-lineages/all-serotypes/README.md rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/README.md diff --git a/data/community/dengue-lineages/all-serotypes/denv1/CHANGELOG.md b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/CHANGELOG.md similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv1/CHANGELOG.md rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/CHANGELOG.md diff --git a/data/community/dengue-lineages/all-serotypes/denv1/README.md b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/README.md similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv1/README.md rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/README.md diff --git a/data/community/dengue-lineages/all-serotypes/denv1/genome_annotation.gff3 b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/genome_annotation.gff3 similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv1/genome_annotation.gff3 rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/genome_annotation.gff3 diff --git a/data/community/dengue-lineages/all-serotypes/denv1/pathogen.json b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/pathogen.json similarity index 96% rename from data/community/dengue-lineages/all-serotypes/denv1/pathogen.json rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/pathogen.json index 560eb3f7..8521ad24 100644 --- a/data/community/dengue-lineages/all-serotypes/denv1/pathogen.json +++ b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/pathogen.json @@ -25,6 +25,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -51,7 +52,7 @@ "privateMutations": { "cutoff": 25, "enabled": true, - "typical": 10, + 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rename from data/community/dengue-lineages/all-serotypes/denv1/tree.json rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/tree.json diff --git a/data/community/dengue-lineages/all-serotypes/denv2/CHANGELOG.md b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/CHANGELOG.md similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv2/CHANGELOG.md rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/CHANGELOG.md diff --git a/data/community/dengue-lineages/all-serotypes/denv2/README.md b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/README.md similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv2/README.md rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/README.md diff --git a/data/community/dengue-lineages/all-serotypes/denv2/genome_annotation.gff3 b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/genome_annotation.gff3 similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv2/genome_annotation.gff3 rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/genome_annotation.gff3 diff --git a/data/community/dengue-lineages/all-serotypes/denv2/pathogen.json b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/pathogen.json similarity index 96% rename from data/community/dengue-lineages/all-serotypes/denv2/pathogen.json rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/pathogen.json index 4e5f5cfc..565b458c 100644 --- a/data/community/dengue-lineages/all-serotypes/denv2/pathogen.json +++ b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/pathogen.json @@ -25,6 +25,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -51,7 +52,7 @@ "privateMutations": { "cutoff": 25, "enabled": true, - "typical": 10, + "typical": 15, "weightLabeledSubstitutions": 2, "weightReversionSubstitutions": 1, "weightUnlabeledSubstitutions": 1 diff --git a/data/community/dengue-lineages/all-serotypes/denv2/reference.fasta b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/reference.fasta similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv2/reference.fasta rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/reference.fasta diff --git a/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/sequences.fasta b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/sequences.fasta new file mode 100755 index 00000000..a66cd8b3 --- /dev/null +++ b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/sequences.fasta @@ -0,0 +1,11640 @@ +>PP292049.1|2024-01 +------------------------------------------------------------ +------------------------------------------------------------ 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+------------------------------------------------------------ +------------------------------------------------------------ +-----------------acagtctggaacagggtgtggattcaagaaaacccatggatgg +aagataaaactccagtagaatcatggga--ggaaatcccatatttgggaaaaagagaaga +ccaatggtgcggctcattgatcgggctaacaagcagggccacttgggcaaagaacatcca +aacagcaataaatcaagttagatccctaataggcaatgaggaatacacagactacatg-- +-----ccatccatgaaaaggttcagaagagaagag------------gaagaggcaggag +tcttgtggtag------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---- +>MN448851.1|2011-09-23 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+------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------acagtttggaacagggtgtggattcaagaaaacccatggatgg +aagacaaaactccagtagaatcatggga--ggaaatcccgtatttgggaaaaagagaaga +ccaatggtgcggctcattgattgggctaacaagcagggctacctgggcaaagaacatcca +aacagcaataaatcaagttagatccctaataggcaatgaggaatacacagactacatg-- +-----ccatccatgaaaagattcaggagagaagag------------gaagaggcaggag +tcttgtggtag------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ 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+------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------acagtctggaacagggtgtggattcaagaaaacccatggatgg +aagacaaaactccagtggaatcatggga--ggaaatcccatacttggggaaaagagaaga +ccaatggtgcggctcattgatagggttaacaagcagagccacctgggcaaagaacatcca +aacagcaataaaccaagttagatccttaataggcagtgaggaatacacagactatatg-- +-----ccatccatgaaaagattcagaagagaagag------------gaagaggcagggg +tcttgtggtag------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---- +>MH822954.1|2015-08-31 +------------------------------------------------------------ +---------------------------------------------atgaataaccaacgg +aaaaaggcgagaaatacgcctttcaatatgctgaaacgcgagagaaaccgcgtgtcgact +gtgcaacagttgacaaagagattctcacttggaatgctgcagggacgaggaccattgaaa +ctgttcatggccctggtggcattccttcgtttcctaacaatcccaccaacagcagggata +ctgaaaagatggggaacgatcaaaaagtcaaaggctatcaatgtcttgagaggctttagg +aaagagattggaaggatgctgaatatcttgaataggagacgcagaactgtaggcatgatc +atcatgctgattccaacagcaatggcgttccatttaaccacacgcaatggagaaccacac +atgatcgtcagcagacaagagaaagggaaaagtctcttgtttaaaacagaggatggtgtg +aacatgtgtaccctcatggccatggaccttggtgaactgtgtgaagacacagtcacttat +aactgtcctcttctcaggcagaatgaaccagaagacatagactgctggtgcaactccacg +tccacatgggtaacttatgggacatgcactgccacaggagaacacagaagggaaaaaaga +tcagtggcactcgtcccacatgtgggaatgggattggagacacgaactgaaacatggatg 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+------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------acagtctggaacagggtgtggattcaagaaaacccatggatgg +aagacaaaactctagtagaatcatggga--agaaatcccatatttggggaaaagagaaga +ccaatggtgcggctcattgattgggctaacaagcagggccacctgggcgaagaacatcca +aacagcgataaatcaagttagatccctaataggcaatgaggaatacacagactacatg-- +-----ccatccatgaaaagattcagaagagaagag------------gaagaggcaggag +tcttgtggtag------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ 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+------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------gcagtctggaatagggtgtggatccaggaaaacccttggatgg +aagacaaaactccagtggaatcatggga--agaagtcccatacttggggaaaagagaaga +ccaatggtgcggttcattgattgggctaacaagcagggccacctgggcaaagaacatcca +aacagcaataaatcaagtcagatcccttataggcaatgaggaatacacagactacatg-- +-----ccatccatgaagagattcagaagggaagag------------gaagaggccggtg +tcctgtggtag------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ 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+-----ccatccatgaaaagattcagaagagaagag------------gaagaggcaggag +ttttgtggtag------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---- diff --git a/data/community/dengue-lineages/all-serotypes/denv2/tree.json b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/tree.json similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv2/tree.json rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/tree.json diff --git a/data/community/dengue-lineages/all-serotypes/denv3/CHANGELOG.md b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/CHANGELOG.md similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv3/CHANGELOG.md rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/CHANGELOG.md diff --git a/data/community/dengue-lineages/all-serotypes/denv3/README.md b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/README.md similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv3/README.md rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/README.md diff --git a/data/community/dengue-lineages/all-serotypes/denv3/genome_annotation.gff3 b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/genome_annotation.gff3 similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv3/genome_annotation.gff3 rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/genome_annotation.gff3 diff --git a/data/community/dengue-lineages/all-serotypes/denv3/pathogen.json b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/pathogen.json similarity index 96% rename from data/community/dengue-lineages/all-serotypes/denv3/pathogen.json rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/pathogen.json index a04d95b6..1cc0c5e1 100644 --- a/data/community/dengue-lineages/all-serotypes/denv3/pathogen.json +++ b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/pathogen.json @@ -25,6 +25,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -51,7 +52,7 @@ "privateMutations": { "cutoff": 25, "enabled": true, - "typical": 10, + "typical": 15, "weightLabeledSubstitutions": 2, "weightReversionSubstitutions": 1, "weightUnlabeledSubstitutions": 1 diff --git a/data/community/dengue-lineages/all-serotypes/denv3/reference.fasta b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/reference.fasta similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv3/reference.fasta rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/reference.fasta diff --git a/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/sequences.fasta b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/sequences.fasta new file mode 100755 index 00000000..ed5f91da --- /dev/null +++ b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/sequences.fasta @@ -0,0 +1,4320 @@ +>OR394012.1|2019-10-29 +------------------------------------------------------------ +----------------------------------atgaacaaccaacggaaaaagacggg +aaaaccgtctatcaatatgctgaaacgcgtgagaaaccgtgtgtcaactggatcacagtt +ggcgaagagattctcaagaggactgctgaatggccaaggaccaatgaaattggttatggc +gttcatagctttcctcagatttctagccattccaccgacagcgggaatcttggctagatg 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+------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------- diff --git a/data/community/dengue-lineages/all-serotypes/denv3/tree.json b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/tree.json similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv3/tree.json rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/tree.json diff --git a/data/community/dengue-lineages/all-serotypes/denv4/CHANGELOG.md b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/CHANGELOG.md similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv4/CHANGELOG.md rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/CHANGELOG.md diff --git a/data/community/dengue-lineages/all-serotypes/denv4/README.md b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/README.md similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv4/README.md rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/README.md diff --git a/data/community/dengue-lineages/all-serotypes/denv4/genome_annotation.gff3 b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/genome_annotation.gff3 similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv4/genome_annotation.gff3 rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/genome_annotation.gff3 diff --git a/data/community/dengue-lineages/all-serotypes/denv4/pathogen.json b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/pathogen.json similarity index 96% rename from data/community/dengue-lineages/all-serotypes/denv4/pathogen.json rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/pathogen.json index 4847c303..9edc0d43 100644 --- a/data/community/dengue-lineages/all-serotypes/denv4/pathogen.json +++ b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/pathogen.json @@ -25,6 +25,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -51,7 +52,7 @@ "privateMutations": { "cutoff": 25, "enabled": true, - "typical": 10, + "typical": 15, "weightLabeledSubstitutions": 2, "weightReversionSubstitutions": 1, "weightUnlabeledSubstitutions": 1 diff --git a/data/community/dengue-lineages/all-serotypes/denv4/reference.fasta b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/reference.fasta similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv4/reference.fasta rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/reference.fasta diff --git a/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/sequences.fasta b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/sequences.fasta new file mode 100755 index 00000000..156a1b58 --- /dev/null +++ b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/sequences.fasta @@ -0,0 +1,3179 @@ +>OP811967.1|2019-08-20 +------------------------------------------------------------ +------------------------------------------atgaaccaacgaaaaaag +gtggttagaccacctttcaatatgctgaaacgcgagagaaaccgcgtatcaacccctcaa +gggttggtgaagagattctcaaccggacttttttctgggaaaggacccttacggatggtg +ctagcactcatcacgtttttgcgagtcctttccatcccaccaacagcagggattctgaag +agatggggacagttgaagaaaaataaggccatcaagatactgattggattcaggaaggag +ataggccgcatgctgaacatcttgaacgggagaaaaaggtcaacgataacattgttgtgc +ttgattcccaccgtaatggcgtttcacttatcaacaagagatggcgaacccctcatgata +gtggcaaaacatgaaagggggagacctctcttgtttaagacaacagaggggatcaacaaa +tgcactctcattgccatggacttgggtgaaatgtgtgaggacactgtcacgtacaaatgc +cccctactggtcaatactgaacctgaagacattgattgctggtgcaacctcacatctacc 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b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/tree.json similarity index 100% rename from data/community/dengue-lineages/all-serotypes/denv4/tree.json rename to data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/tree.json From 96027981009a7b2441ff7ed3df0f4c40a9c28708 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Tue, 13 Aug 2024 15:03:52 +0200 Subject: [PATCH 03/26] chore: rebuild [skip ci] --- data/community/collection.json | 6 +- .../denv1/unreleased/CHANGELOG.md | 5 + .../all-serotypes/denv1/unreleased/README.md | 27 + .../denv1/unreleased/dataset.zip | Bin 0 -> 3681816 bytes .../denv1/unreleased/genome_annotation.gff3 | 15 + .../denv1/unreleased/pathogen.json | 85 + .../denv1/unreleased/reference.fasta | 156 + .../denv1/unreleased/sequences.fasta | 7964 + .../all-serotypes/denv1/unreleased/tree.json | 44660 +++++ .../denv2/unreleased/CHANGELOG.md | 5 + .../all-serotypes/denv2/unreleased/README.md | 28 + .../denv2/unreleased/dataset.zip | Bin 0 -> 4787646 bytes .../denv2/unreleased/genome_annotation.gff3 | 15 + .../denv2/unreleased/pathogen.json | 85 + .../denv2/unreleased/reference.fasta | 156 + .../denv2/unreleased/sequences.fasta | 11640 ++ .../all-serotypes/denv2/unreleased/tree.json | 58440 +++++++ .../denv3/unreleased/CHANGELOG.md | 5 + .../all-serotypes/denv3/unreleased/README.md | 27 + .../denv3/unreleased/dataset.zip | Bin 0 -> 1736860 bytes .../denv3/unreleased/genome_annotation.gff3 | 15 + .../denv3/unreleased/pathogen.json | 85 + .../denv3/unreleased/reference.fasta | 155 + .../denv3/unreleased/sequences.fasta | 4320 + .../all-serotypes/denv3/unreleased/tree.json | 23644 +++ .../denv4/unreleased/CHANGELOG.md | 5 + .../all-serotypes/denv4/unreleased/README.md | 27 + .../denv4/unreleased/dataset.zip | Bin 0 -> 1483393 bytes .../denv4/unreleased/genome_annotation.gff3 | 15 + .../denv4/unreleased/pathogen.json | 85 + .../denv4/unreleased/reference.fasta | 155 + .../denv4/unreleased/sequences.fasta | 3179 + 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a/data/community/collection.json +++ b/data/community/collection.json @@ -23,6 +23,10 @@ "community/moncla-lab/iav-h5/2.3.2.1", "community/moncla-lab/iav-h5/ha/2.3.4.4", "community/moncla-lab/iav-h5/ha/all-clades", - "community/moncla-lab/iav-h5/ha/2.3.2.1" + "community/moncla-lab/iav-h5/ha/2.3.2.1", + "community/v-gen-lab/dengue-lineages/all-serotypes/denv1", + "community/v-gen-lab/dengue-lineages/all-serotypes/denv4", + "community/v-gen-lab/dengue-lineages/all-serotypes/denv2", + "community/v-gen-lab/dengue-lineages/all-serotypes/denv3" ] } diff --git a/data_output/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/unreleased/CHANGELOG.md b/data_output/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/unreleased/CHANGELOG.md new file mode 100644 index 00000000..495dc86a --- /dev/null +++ b/data_output/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/unreleased/CHANGELOG.md @@ -0,0 +1,5 @@ +## Unreleased + +Initial release of a DENV-1 dataset for Lineage classification! + +Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/unreleased/README.md b/data_output/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/unreleased/README.md new file mode 100644 index 00000000..a04465cc --- /dev/null +++ b/data_output/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/unreleased/README.md @@ -0,0 +1,27 @@ +# Nextclade dataset for "DENV-1 Lineages" based on reference "NC_001477.1" + + +## Dataset attributes + +| attribute | value | +| -------------------- | ---------------------------------------- | +| name | DENV-1 | +| refName | NC_001477 | +| refAccession | NC_001477.1 | + +## Scope of this Dataset +This dataset is based on the dengue virus lineage system from [Verity et al., 2024](https://doi.org/10.1101/2024.05.16.24307504) and is suitable for the analysis of DENV-1 viral sequences. The systems are independent, so sequences from other serotypes may not be classified or may be assigned as "Outgroup." + +## Authors and contacts + +Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri). + +## Dengue Lineages System Project + +This system is built off experience developing lineage systems for other viruses of public health importance, and is the result of a global collaboration of researchers and public health professionals. It aims to provide additional spatial and temporal resolution with which to discuss the large genetic diversity of dengue virus. Specifically, it splits up existing genotypes into smaller groups and provides a standardized, neutral naming system. + +Broadly speaking, we define major and minor lineages within each genotype. These lineages are defined by the same rules, but use different nomenclature. In theory, minor lineages should be more useful for country-specific questions, and major lineages for regional questions. Of course, it won't always necessarily work like that - some minor lineages are very widespread, and some major lineages are geographically limited. + +## 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/v-gen-lab/dengue-lineages/all-serotypes/denv1/unreleased/dataset.zip b/data_output/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/unreleased/dataset.zip new file mode 100644 index 0000000000000000000000000000000000000000..000c0662cae21dc252facbaecd299b052bd48b13 GIT binary patch literal 3681816 zcmeF(&5os4dgb?mZMeaN4Nr_7M^gj4?IMd`Ra6OZ18hoWf9T7qYW1Mq5TcSnGNoiD zJ2R+K+3JDenXkZrFTw*4Y-;R`SfG<+An2LFF+zma6ISS6|5ZS+7VPP}Kodq2-w z>sil!-*X}|$lw2m|MtK0AAaXN{?>Q?#sBc%{V)Hb6W{+{-yi#}`{>Qj zKmN5}yZJ}YUfeysyM1~0@uNq7|JjrKC$~>;u9=(XpWNKu{N``{?jOGK_RYt)_XXYG zeDeIo&2K+>c6a;f-Ob~tw=Z8l`Q*vt+xsWapZ%>zkN)89_T!t+pTD@fx&6uWFYj-D 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