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Update datasets
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@corneliusroemer
corneliusroemer committed Nov 16, 2024
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5 changes: 5 additions & 0 deletions data/nextstrain/mpox/all-clades/CHANGELOG.md
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## Unreleased

- 11 newly designated B.1 sublineages are now included. See <https://github.com/mpxv-lineages/lineage-designation/pull/45> for details.
- Newly shared sequences are now included

## 2024-08-27T21:28:04Z

- Clade Ia and clade Ib are now distinguished
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2 changes: 1 addition & 1 deletion data/nextstrain/mpox/all-clades/tree.json
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4 changes: 4 additions & 0 deletions data/nextstrain/mpox/clade-i/CHANGELOG.md
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## Unreleased

- Newly shared sequences are now included

## 2024-08-01T22:31:31Z

Initial release of this dataset.
2 changes: 1 addition & 1 deletion data/nextstrain/mpox/clade-i/tree.json
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6 changes: 6 additions & 0 deletions data/nextstrain/mpox/clade-iib/CHANGELOG.md
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## Unreleased

- 11 newly designated B.1 sublineages are now included. See <https://github.com/mpxv-lineages/lineage-designation/pull/45> for details.
- Newly shared sequences are now included
- The cluster QC metric's window size has been broadened to detect clusters that span a region of up to 1000bp (up from 100bp)

## 2024-04-19T07:50:39Z

- New hMPXV-1 lineages B.1.21, B.1.22, and C.1.1 are now included in the dataset. For more information on these lineages, see the [hMPXV-1 lineage definitions PR](https://github.com/mpxv-lineages/lineage-designation/pull/37)
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9 changes: 6 additions & 3 deletions data/nextstrain/mpox/clade-iib/pathogen.json
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"snpClusters": {
"clusterCutOff": 5,
"enabled": true,
"scoreWeight": 20,
"windowSize": 100
"scoreWeight": 10,
"windowSize": 1000
},
"stopCodons": {
"enabled": true,
Expand All @@ -88,5 +88,8 @@
"schemaVersion": "3.0.0",
"shortcuts": [
"hMPXV"
]
],
"version": {
"tag": "unreleased"
}
}
2 changes: 1 addition & 1 deletion data/nextstrain/mpox/clade-iib/reference.fasta
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2 changes: 1 addition & 1 deletion data/nextstrain/mpox/clade-iib/tree.json
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6 changes: 6 additions & 0 deletions data/nextstrain/mpox/lineage-b.1/CHANGELOG.md
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## Unreleased

- 11 newly designated B.1 sublineages are now included. See <https://github.com/mpxv-lineages/lineage-designation/pull/45> for details.
- Newly shared sequences are now included
- The cluster QC metric's window size has been broadened to detect clusters that span a region of up to 1000bp (up from 100bp)

## 2024-04-19T07:50:39Z

- New hMPXV-1 lineages B.1.21, B.1.22, and C.1.1 are now included in the dataset. For more information on these lineages, see the [hMPXV-1 lineage definitions PR](https://github.com/mpxv-lineages/lineage-designation/pull/37)
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277 changes: 73 additions & 204 deletions data/nextstrain/mpox/lineage-b.1/pathogen.json
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"official": true,
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"snpClusters": {
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"enabled": true,
"scoreWeight": 20,
"windowSize": 100
"scoreWeight": 10,
"windowSize": 1000
},
"stopCodons": {
"enabled": true,
Expand All @@ -280,5 +146,8 @@
"schemaVersion": "3.0.0",
"shortcuts": [
"hMPXV_B1"
]
],
"version": {
"tag": "unreleased"
}
}
2 changes: 1 addition & 1 deletion data/nextstrain/mpox/lineage-b.1/tree.json
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