Global tree and separating out the WA-specific configs #30
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
…pecific build configuration Subsequent commits will place the washington state specific configs and rules in this directory.
This separates the washginton-specific rules and configs from the new global workflow. Subsequent commits will tune global rules and configs, and rooting. The washginton-specific workflow can run via: nextstrain build phylogenetic --configfile build-configs/washington-state/config.yaml
Use AF260968 ('Egypt 1951') as the global reference and root, following Mencattelli et al, 2023
https://www.nature.com/articles/s41467-023-42185-7
…n phylogenetic analyses
Exclude several PAT strains that did not have the is_lab_host metadata field set to True. Exclude several strains that were either putative recombinants or were below the PAT FV537222 cluster.
Separate washington-state specific refine parameters from a more permissive global refine parameters.
|
Rooted global tree can be previewed here: https://next.nextstrain.org/staging/WNV/global/rooted |
j23414
changed the title
|
Cool! Small note that something is fairly off in terms of molecular clock. You can see here https://nextstrain.org/staging/WNV/global/rooted?f_country=USA that the main USA clade has a common ancestor of ~1400 AD, while it should be ~1998. You can perhaps better see the correspondence here: https://nextstrain.org/staging/WNV/global/rooted:WNV/NA |
|
We're planning to fix the molecular clock or decide to split into lineage trees in a later PR (will write up a GitHub issue). Merging this to have a draft split of WA and global config files. |
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.
Description of proposed changes
Separate out the WA-specific configs and some fine-tuning of the global tree.
Related issue(s)
Checklist