Merge pull request #452 from nextstrain/bdbv-update

Bdbv update

Author: rneher

data/nextstrain/orthoebolavirus/bdbv/CHANGELOG.md

@@ -1 +1,10 @@
+## Unreleased
+
+- Add outbreak annotation
+- add GP_003:367 to known stop codons
+- Include 2026 genomes
+
+
 ## 2026-05-15T16:16:45Z
+
+Initial release of this dataset.

data/nextstrain/orthoebolavirus/bdbv/README.md

@@ -7,9 +7,9 @@
 | nextclade dataset path | nextstrain/orthoebolavirus/bdbv                     |
 | annotation             | [NC_014373.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_014373.1)                   |
 
-This Nextclade dataset for Bundibugyo virus [(Orthoebolavirus bundibugyoense)](https://ictv.global/report/chapter/filoviridae/filoviridae/orthoebolavirus) aligns to the reference sequence [NC_014373.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_014373) and translates major CDS. It scores the sequence with respect to unexpected frameshifts or stop codons, missing sequence (in form of `NNN`s) and mixed bases. Outbreak annotations, as well as refined QC scores are planned additions for the future.
+This Nextclade dataset for Bundibugyo virus [(Orthoebolavirus bundibugyoense)](https://ictv.global/report/chapter/filoviridae/filoviridae/orthoebolavirus) aligns to the reference sequence [NC_014373.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_014373) and translates major CDS. It scores the sequence with respect to unexpected frameshifts or stop codons, missing sequence (in form of `NNN`s) and mixed bases.
 
-For more information on Ebola viruses, see [ViralZone](https://viralzone.expasy.org/207).
+Data from the 2026 outbreak were generously shared by the groups of Prof. Placide Mbala-Kingebeni (INRB, DRC) and Dr Isaac Ssewanyana (CPHL, Uganda) to facilitate the public health response and containment of the virus. These data are described in a post on [Virological.org](https://virological.org/t/initial-genomes-from-may-2026-bundibugyo-virus-disease-outbreak-in-the-democratic-republic-of-the-congo-and-uganda/1032) and were deposited in Pathoplexus under [Restricted Data-Use terms](https://pathoplexus.org/about/terms-of-use/restricted-data). Please consult the authors and the [data-use terms](https://pathoplexus.org/about/terms-of-use/restricted-data) before using these sequences.
 
 
 

data/nextstrain/orthoebolavirus/bdbv/pathogen.json

@@ -6,7 +6,8 @@
     "allowedMismatches": 10,
     "windowSize": 40,
     "minSeedCover": 0.03,
-    "gapAlignmentSide": "left"
+    "gapAlignmentSide": "left",
+    "retryReverseComplement": true
   },
   "attributes": {
     "name": "Bundibugyo ebolavirus",
@@ -59,13 +60,13 @@
     },
     "stopCodons": {
       "enabled": true,
-      "ignoredStopCodons": [],
+      "ignoredStopCodons": [{"cdsName": "GP_003", "codon": 366}],
       "scoreWeight": 20
     }
   },
   "schemaVersion": "3.0.0",
   "shortcuts": [
-    "nextstrain/ebola/bebov"
+    "nextstrain/ebola/bdbv"
   ],
   "version": {
     "updatedAt": "2026-04-14T11:55:23Z",

data/nextstrain/orthoebolavirus/bdbv/tree.json

@@ -2317,7 +2317,7 @@
         {
           "path": "nextstrain/orthoebolavirus/bdbv",
           "shortcuts": [
-            "nextstrain/ebola/bebov"
+            "nextstrain/ebola/bdbv"
           ],
           "attributes": {
             "name": "Bundibugyo ebolavirus",
@@ -2335,6 +2335,9 @@
             "reference": "reference.fasta"
           },
           "capabilities": {
+            "customClades": {
+              "outbreak": 4
+            },
             "qc": [
               "frameShifts",
               "missingData",
@@ -2344,6 +2347,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2026-05-15T16:16:45Z",
               "tag": "2026-05-15--16-16-45Z",
@@ -2354,8 +2364,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2026-05-15T16:16:45Z",
-            "tag": "2026-05-15--16-16-45Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"

data_output/index.json

@@ -0,0 +1,10 @@
+## Unreleased
+
+- Add outbreak annotation
+- add GP_003:367 to known stop codons
+- Include 2026 genomes
+
+
+## 2026-05-15T16:16:45Z
+
+Initial release of this dataset.

data_output/nextstrain/orthoebolavirus/bdbv/unreleased/CHANGELOG.md

@@ -0,0 +1,15 @@
+# Nextclade dataset for Bundibugyo virus (Orthoebolavirus bundibugyoense)
+
+| Key                    | Value                                                                           |
+| ---------------------- | ------------------------------------------------------------------------------- |
+| authors                | [Richard Neher](https://neherlab.org) |
+| data source            | Genbank                                             |
+| nextclade dataset path | nextstrain/orthoebolavirus/bdbv                     |
+| annotation             | [NC_014373.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_014373.1)                   |
+
+This Nextclade dataset for Bundibugyo virus [(Orthoebolavirus bundibugyoense)](https://ictv.global/report/chapter/filoviridae/filoviridae/orthoebolavirus) aligns to the reference sequence [NC_014373.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_014373) and translates major CDS. It scores the sequence with respect to unexpected frameshifts or stop codons, missing sequence (in form of `NNN`s) and mixed bases.
+
+Data from the 2026 outbreak were generously shared by the groups of Prof. Placide Mbala-Kingebeni (INRB, DRC) and Dr Isaac Ssewanyana (CPHL, Uganda) to facilitate the public health response and containment of the virus. These data are described in a post on [Virological.org](https://virological.org/t/initial-genomes-from-may-2026-bundibugyo-virus-disease-outbreak-in-the-democratic-republic-of-the-congo-and-uganda/1032) and were deposited in Pathoplexus under [Restricted Data-Use terms](https://pathoplexus.org/about/terms-of-use/restricted-data). Please consult the authors and the [data-use terms](https://pathoplexus.org/about/terms-of-use/restricted-data) before using these sequences.
+
+
+