You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: phylogenetic/README.md
+13Lines changed: 13 additions & 0 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -26,6 +26,19 @@ The resulting datasets can be viewed in a web browser:
26
26
nextstrain view phylogenetic/outbreak-specific
27
27
```
28
28
29
+
There are currently two datasets configured, and each is a work in progress.
30
+
31
+
#### Ebov-2013 / West-Africa 2014
32
+
33
+
* The temporal analysis is wrong (root pushed back), which I think is due to the inclusion of relapse cases. We could try specifying a rate or explore ways to infer the rate based on a subset of samples within treetime.
34
+
* Missing colors & lat-longs. Some of this is misspelt geographical metadata to be fixed in ingest.
35
+
* Alignment (mafft) takes a long time cf. nextclade alignment. We should compare the two approaches.
36
+
37
+
#### Ebov-2025
38
+
39
+
* Currently (2025-09-29) there are 4 available genomes. At this time [this virological post](https://virological.org/t/the-16th-ebola-virus-disease-outbreak-in-bulape-health-zone-kasai-democratic-republic-of-the-congo-a-new-spillover-event-from-an-unknown-reservoir-host/1003) is a better summary of the genomic situation.
40
+
41
+
29
42
### All-outbreaks
30
43
31
44
This workflow subsamples genomes across outbreaks to present an overview of the known genomic history
0 commit comments