Merge branch 'nextstrain:master' into master

data/nextstrain/mpox/all-clades/CHANGELOG.md

@@ -1,3 +1,8 @@
+## Unreleased
+
+- Clade Ia and clade Ib are now distinguished
+- Sequences shared via Genbank since 2024 have been added
+
 ## 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)
@@ -16,3 +21,4 @@ Some genes have been renamed and one has been added. The new annotation is based
 - 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
+

data/nextstrain/mpox/all-clades/README.md

@@ -1,24 +1,24 @@
 # 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`        |
+| 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`<br>Mpox virus (Clade I): `nextstrain/mpox/clade-i` |
 
 ## Scope of this dataset
 
-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`).
+This dataset is for Mpox viruses of all clades (Ia, Ib, 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`). For clade I sequences, you may want to use the dataset "Clade I" (`nextstrain/mpox/clade-i`).
 
 ## Reference sequence and reference tree
 
 The reference used in this dataset is the clade IIb NCBI refseq `NC_063383.1` (Isolate `MPXV-M5312_HM12_Rivers`).
 
-Sequences for the reference tree come from NCBI/Genbank and are downsampled to around 500 sequences from the diversity of clades, lineages, countries and collection dates.
+Sequences for the reference tree come from NCBI/Genbank and are downsampled to around 900 sequences from the diversity of clades, lineages, countries and collection dates.
 
 ## Further reading
 

data/nextstrain/mpox/all-clades/pathogen.json

@@ -173,10 +173,10 @@
       "weightUnlabeledSubstitutions": 1
     },
     "snpClusters": {
-      "clusterCutOff": 10,
-      "enabled": false,
+      "clusterCutOff": 5,
+      "enabled": true,
       "scoreWeight": 10,
-      "windowSize": 100
+      "windowSize": 300
     },
     "stopCodons": {
       "enabled": true,
@@ -209,5 +209,8 @@
   "shortcuts": [
     "MPXV",
     "nextstrain/mpox"
-  ]
+  ],
+  "version": {
+    "tag": "unreleased"
+  }
 }

data_output/index.json

@@ -1720,7 +1720,7 @@
             "treeJson": "tree.json"
           },
           "capabilities": {
-            "clades": 5,
+            "clades": 7,
             "customClades": {
               "outbreak": 1,
               "lineage": 33
@@ -1730,10 +1730,18 @@
               "missingData",
               "mixedSites",
               "privateMutations",
+              "snpClusters",
               "stopCodons"
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2024-04-19T07:50:39Z",
               "tag": "2024-04-19--07-50-39Z",
@@ -1752,8 +1760,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2024-04-19T07:50:39Z",
-            "tag": "2024-04-19--07-50-39Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"

data_output/nextstrain/mpox/all-clades/unreleased/CHANGELOG.md

@@ -0,0 +1,24 @@
+## Unreleased
+
+- Clade Ia and clade Ib are now distinguished
+- Sequences shared via Genbank since 2024 have been added
+
+## 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)
+- The sequences used in the reference trees have been updated to include the latest sequences available in Genbank as of 2024-04-16
+
+## 2024-01-16T20:31:02Z
+
+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
+

data_output/nextstrain/mpox/all-clades/unreleased/README.md

@@ -0,0 +1,27 @@
+# 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`<br>Mpox virus (Clade I): `nextstrain/mpox/clade-i` |
+
+## Scope of this dataset
+
+This dataset is for Mpox viruses of all clades (Ia, Ib, 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`). For clade I sequences, you may want to use the dataset "Clade I" (`nextstrain/mpox/clade-i`).
+
+## Reference sequence and reference tree
+
+The reference used in this dataset is the clade IIb NCBI refseq `NC_063383.1` (Isolate `MPXV-M5312_HM12_Rivers`).
+
+Sequences for the reference tree come from NCBI/Genbank and are downsampled to around 900 sequences from the diversity of clades, lineages, countries and collection dates.
+
+## Further reading
+
+The lineage system used is described 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).
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html