Add v3 mpxv datasets, still some wip (#104)

* Add v3 mpxv datasets, still some wip * fix: Update nextstrain collection with new mpox dataset paths * chore: rebuild [skip ci] * Update mpox datasets * chore: rebuild [skip ci] --------- Co-authored-by: nextstrain-bot <[email protected]>
nextstrain · Nov 21, 2023 · 2008684 · 2008684
1 parent 5e2742c
commit 2008684
Show file tree

Hide file tree

Showing 81 changed files with 5,661 additions and 352,298 deletions.
diff --git a/data/nextstrain/collection.json b/data/nextstrain/collection.json
@@ -34,9 +34,9 @@
     "nextstrain/flu/yam/ha/JN993010",
     "nextstrain/rsv/a/EPI_ISL_412866",
     "nextstrain/rsv/b/EPI_ISL_1653999",
-    "nextstrain/mpx/hmpxv-b1/pseudo_ON563414",
-    "nextstrain/mpx/hmpxv/NC_063383.1",
-    "nextstrain/mpx/mpxv/ancestral",
+    "nextstrain/mpox/all-clades",
+    "nextstrain/mpox/clade-iib",
+    "nextstrain/mpox/lineage-b.1",
     "nextstrain/ebola/zaire",
     "nextstrain/enterovirus/d68/fermon",
     "nextstrain/hiv/1",

diff --git a/data/nextstrain/mpox/all-clades/CHANGELOG.md b/data/nextstrain/mpox/all-clades/CHANGELOG.md
@@ -0,0 +1,13 @@
+## Unreleased
+
+Initial release of this dataset. This dataset is similar to the v2 dataset [`MPXV/ancestral`](https://github.com/nextstrain/nextclade_data/tree/2023-08-17--15-51-24--UTC/data/datasets/MPXV/references/ancestral/versions/2023-08-01T12%3A00%3A00Z/files) with some differences.
+
+### New and changed gene names
+
+Some genes have been renamed and one has been added. The new annotation is based on NCBI refseq annotations that were released in November 2022. The v2 dataset predates this refseq:
+
+- The 4 genes in the inverted terminal repeat segment (ITR) on both ends of the genome (OPG001, OPG002, OPG003,OPG015) are now all included. The genes on the 3' end (~positions 190000-197000) now have an `_dup` appended to distinguish them.
+- The gene previously named `NBT03_gp052` is now called `OPG073`
+- The gene previously named `NBT03_gp174` is now called `OPG016`
+- The gene previously named `NBT03_gp175` is now called `OPG015_dup`
+- Gene `OPG166` has been added
diff --git a/data/nextstrain/mpox/all-clades/README.md b/data/nextstrain/mpox/all-clades/README.md
@@ -0,0 +1,23 @@
+# Nextclade dataset for "Mpox virus (All Clades)"
+
+| Key                    | Value                                                                                                                 |
+| ---------------------- | --------------------------------------------------------------------------------------------------------------------- |
+| authors                | [Cornelius Roemer](https://neherlab.org), [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org) |
+| data source            | Genbank                                                                                                               |
+| workflow               | [github.com/nextstrain/mpox/nextclade](https://github.com/nextstrain/mpox/nextclade)                                  |
+| nextclade dataset path | nextstrain/mpox/all-clades                                                                                            |
+| annotation             | [NC_063383.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_063383)                                                         |
+| clade definitions      | [github.com/mpxv-lineages/lineage-designation](https://github.com/mpxv-lineages/lineage-designation)                  |
+| related datasets       | Mpox virus (Clade IIb): `nextstrain/mpox/clade-iib`<br> Mpox virus (Lineage B.1) `nextstrain/mpox/lineage-b.1`        |
+
+This dataset is for Mpox viruses of all clades (I, IIa and IIb). For a focused analysis of sequences from clade IIb, you may want to use the more specific dataset: "Clade IIb" (`nextstrain/mpox/clade-iib`). For an even more focused analysis of 2022-2023 outbreak sequences (lineage B.1 and sublineages), you may want to use the even more specific dataset: "Lineage B.1" (`nextstrain/mpox/lineage-b.1`).
+
+The lineage system used is defined in [Happi et al. (2022)](https://doi.org/10.1371/journal.pbio.3001769). Lineage definitions are available at [github.com/mpxv-lineages/lineage-designation](https://github.com/nextstrain/mpox/nextclade).
+
+The reference used in this dataset is the clade IIb NCBI refseq `NC_063383.1` (Isolate `MPXV-M5312_HM12_Rivers`).
+
+The reference tree consists of around 500 sequences with representatives from all clades and lineages.
+
+## Further reading
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data/nextstrain/mpox/all-clades/genome_annotation.gff3 b/data/nextstrain/mpox/all-clades/genome_annotation.gff3
diff --git a/data/nextstrain/mpox/all-clades/pathogen.json b/data/nextstrain/mpox/all-clades/pathogen.json
@@ -0,0 +1,212 @@
+{
+  "alignmentParams": {
+    "excessBandwidth": 100,
+    "terminalBandwidth": 300,
+    "allowedMismatches": 8,
+    "windowSize": 40,
+    "minSeedCover": 0.1,
+    "gapAlignmentSide": "left"
+  },
+  "attributes": {
+    "name": "Mpox virus (All clades)",
+    "reference accession": "NC_063383.1",
+    "reference name": "MPXV-M5312_HM12_Rivers"
+  },
+  "compatibility": {
+    "cli": "3.0.0-alpha.0",
+    "web": "3.0.0-alpha.0"
+  },
+  "deprecated": false,
+  "enabled": true,
+  "experimental": false,
+  "files": {
+    "changelog": "CHANGELOG.md",
+    "examples": "sequences.fasta",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "pathogenJson": "pathogen.json",
+    "readme": "README.md",
+    "reference": "reference.fasta",
+    "treeJson": "tree.json"
+  },
+  "official": true,
+  "qc": {
+    "frameShifts": {
+      "enabled": true,
+      "ignoredFrameShifts": [
+        {
+          "codonRange": {
+            "begin": 3,
+            "end": 589
+          },
+          "geneName": "OPG003"
+        },
+        {
+          "codonRange": {
+            "begin": 3,
+            "end": 589
+          },
+          "geneName": "OPG003_dup"
+        },
+        {
+          "codonRange": {
+            "begin": 281,
+            "end": 285
+          },
+          "geneName": "OPG105"
+        },
+        {
+          "codonRange": {
+            "begin": 227,
+            "end": 229
+          },
+          "geneName": "OPG164"
+        },
+        {
+          "codonRange": {
+            "begin": 554,
+            "end": 560
+          },
+          "geneName": "OPG180"
+        },
+        {
+          "codonRange": {
+            "begin": 42,
+            "end": 101
+          },
+          "geneName": "OPG197"
+        },
+        {
+          "codonRange": {
+            "begin": 443,
+            "end": 443
+          },
+          "geneName": "OPG037"
+        },
+        {
+          "codonRange": {
+            "begin": 57,
+            "end": 443
+          },
+          "geneName": "OPG037"
+        },
+        {
+          "codonRange": {
+            "begin": 481,
+            "end": 483
+          },
+          "geneName": "OPG047"
+        },
+        {
+          "codonRange": {
+            "begin": 482,
+            "end": 483
+          },
+          "geneName": "OPG047"
+        },
+        {
+          "codonRange": {
+            "begin": 72,
+            "end": 76
+          },
+          "geneName": "OPG050"
+        },
+        {
+          "codonRange": {
+            "begin": 369,
+            "end": 371
+          },
+          "geneName": "OPG153"
+        },
+        {
+          "codonRange": {
+            "begin": 370,
+            "end": 371
+          },
+          "geneName": "OPG153"
+        },
+        {
+          "codonRange": {
+            "begin": 166,
+            "end": 169
+          },
+          "geneName": "OPG191"
+        },
+        {
+          "codonRange": {
+            "begin": 72,
+            "end": 222
+          },
+          "geneName": "OPG195"
+        },
+        {
+          "codonRange": {
+            "begin": 208,
+            "end": 222
+          },
+          "geneName": "OPG195"
+        },
+        {
+          "codonRange": {
+            "begin": 289,
+            "end": 346
+          },
+          "geneName": "OPG174"
+        }
+      ],
+      "scoreWeight": 20
+    },
+    "missingData": {
+      "enabled": true,
+      "missingDataThreshold": 20000,
+      "scoreBias": 1000
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 40
+    },
+    "privateMutations": {
+      "cutoff": 300,
+      "enabled": true,
+      "typical": 50,
+      "weightLabeledSubstitutions": 6,
+      "weightReversionSubstitutions": 6,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "snpClusters": {
+      "clusterCutOff": 10,
+      "enabled": false,
+      "scoreWeight": 10,
+      "windowSize": 100
+    },
+    "stopCodons": {
+      "enabled": true,
+      "ignoredStopCodons": [
+        {
+          "codon": 187,
+          "geneName": "OPG015_dup"
+        },
+        {
+          "codon": 187,
+          "geneName": "OPG015"
+        },
+        {
+          "codon": 21,
+          "geneName": "OPG176"
+        },
+        {
+          "codon": 299,
+          "geneName": "OPG187"
+        },
+        {
+          "codon": 48,
+          "geneName": "OPG059"
+        }
+      ],
+      "scoreWeight": 20
+    }
+  },
+  "schemaVersion": "3.0.0",
+  "version": {
+    "tag": "unreleased"
+  }
+}
diff --git a/data/nextstrain/mpox/all-clades/reference.fasta b/data/nextstrain/mpox/all-clades/reference.fasta
diff --git a/...strain/mpx/mpxv/ancestral/sequences.fasta → ...extstrain/mpox/all-clades/sequences.fasta b/...strain/mpx/mpxv/ancestral/sequences.fasta → ...extstrain/mpox/all-clades/sequences.fasta
diff --git a/data/nextstrain/mpox/all-clades/tree.json b/data/nextstrain/mpox/all-clades/tree.json
diff --git a/data/nextstrain/mpox/clade-iib/CHANGELOG.md b/data/nextstrain/mpox/clade-iib/CHANGELOG.md
@@ -0,0 +1,13 @@
+## Unreleased
+
+Initial release of this dataset. This dataset is similar to the v2 dataset [`hMPXV/NC_063383.1`](https://github.com/nextstrain/nextclade_data/tree/2023-08-17--15-51-24--UTC/data/datasets/hMPXV/references/NC_063383.1/versions/2023-08-01T12%3A00%3A00Z/files) with some differences.
+
+### New and changed gene names
+
+Some genes have been renamed and one has been added. The new annotation is based on NCBI refseq annotations that were released in November 2022. The v2 dataset predates this refseq:
+
+- The 4 genes in the inverted terminal repeat segment (ITR) on both ends of the genome (OPG001, OPG002, OPG003,OPG015) are now all included. The genes on the 3' end (~positions 190000-197000) now have an `_dup` appended to distinguish them.
+- The gene previously named `NBT03_gp052` is now called `OPG073`
+- The gene previously named `NBT03_gp174` is now called `OPG016`
+- The gene previously named `NBT03_gp175` is now called `OPG015_dup`
+- Gene `OPG166` has been added
diff --git a/data/nextstrain/mpox/clade-iib/README.md b/data/nextstrain/mpox/clade-iib/README.md
@@ -0,0 +1,23 @@
+# Nextclade dataset for "Mpox virus (Clade IIb)"
+
+| Key                    | Value                                                                                                                 |
+| ---------------------- | --------------------------------------------------------------------------------------------------------------------- |
+| authors                | [Cornelius Roemer](https://neherlab.org), [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org) |
+| data source            | Genbank                                                                                                               |
+| workflow               | [github.com/nextstrain/mpox/nextclade](https://github.com/nextstrain/mpox/nextclade)                                  |
+| nextclade dataset path | nextstrain/mpox/clade-iib                                                                                             |
+| annotation             | [NC_063383.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_063383)                                                         |
+| clade definitions      | [github.com/mpxv-lineages/lineage-designation](https://github.com/mpxv-lineages/lineage-designation)                  |
+| related datasets       | Mpox virus (All clades): `nextstrain/mpox/all-clades`<br> Mpox virus (Lineage B.1) `nextstrain/mpox/lineage-b.1`      |
+
+This dataset is for Mpox viruses of clade IIb. A more specific dataset just for outbreak lineage B.1 is available as `nextstrain/mpox/lineage-b.1`. There is also a broader dataset for all clades I, IIa and IIb under `nextstrain/mpox/all-clades`.
+
+The lineage system used is defined in [Happi et al. (2022)](https://doi.org/10.1371/journal.pbio.3001769). Lineage definitions are available at [github.com/mpxv-lineages/lineage-designation](https://github.com/nextstrain/mpox/nextclade).
+
+The reference used in this dataset is the clade IIb NCBI refseq `NC_063383.1` (Isolate `MPXV-M5312_HM12_Rivers`).
+
+The reference tree consists of around 5000 sequences with representatives from all clade IIb lineages.
+
+## Further reading
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html