Use clade I reference KJ642613 for clade I build, mask correctly #292
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
corneliusroemer
changed the title
jameshadfield
approved these changes
Nov 18, 2024
rneher
approved these changes
Nov 20, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
The clade I builds were using the clade IIb reference which is far away.
Switching to a clade I reference makes the trees better.
I curated the mask.bed file by looking at the new alignment, with an eye specifically on fixing clade Ib artefacts. I masked a couple of suspicious regions where there was a mutation right next to a stretch of Ns in sequences of one institution only (usually INRB).
New tree is much more sensible than the old one. The old one had sequences cluster per sequencing institution (INRB vs Erasmus), the new one mixes them nicely as it should.
New build example: https://next.nextstrain.org/staging/mpox/clade-i?c=num_date&label=clade:Ib&m=div
Compare to currently live build which is unrealistic:
https://next.nextstrain.org/staging/mpox/clade-i?c=num_date&label=clade:Ib&m=div
Now one can actually see a time signal of sorts and the root isn't entirely unplausible.
I added a bunch of colorings to allow better investigation of sequencing-institution-specific artefacts/clustering or absence thereof.
We should probably turn off timetree, it's just too wrong, in particular for clade Ib.