Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add E gene builds #17

Closed
j23414 opened this issue Dec 20, 2023 · 5 comments · Fixed by nextstrain/nextstrain.org#771
Closed

Add E gene builds #17

j23414 opened this issue Dec 20, 2023 · 5 comments · Fixed by nextstrain/nextstrain.org#771
Assignees
@j23414
Labels
enhancement New feature or request

Comments

@j23414
Copy link
Contributor

j23414 commented Dec 20, 2023 •
edited

Context

By user request:

Is there any chance we could get a E gene build of nextstrain dengue? Much more sequences of E than full genome, especially in some parts of the world

Description

Examples

Possible steps to a solution

  1. Pull out E gene sequence from the dengue reference.gb file to be used as the reference for the E gene builds.
    a. Or follow rsv rules
  2. Add a filter_length_per_group function for “all_E”, “denv1_E”, “denv2_E”, etc similar to filter_sequences_per_group.
  3. Add E to the dropdown under “Dataset” by appending _E and _genome (e.g. dengue_denv1_genome.json and dengue_denv1_E.json and updating the nextstrain.org manifest file.

Dependencies
@j23414 j23414 added the enhancement New feature or request label Dec 20, 2023
@j23414 j23414 self-assigned this Dec 20, 2023
@j23414 j23414 mentioned this issue Jan 2, 2024
Merged
1 task
@j23414 j23414 linked a pull request Jan 2, 2024 that will close this issue
Update manifest with dengue gene datasets nextstrain/nextstrain.org#771
Merged
1 task
@joverlee521
Copy link
Contributor

joverlee521 commented Jan 3, 2024 •
edited

For posterity, the workflow changes are on the phylogenetic_dir_E branch.

@j23414 j23414 reopened this Jan 3, 2024
@j23414 j23414 mentioned this issue Jan 13, 2024
Closed
1 task
@j23414 j23414 linked a pull request Jan 13, 2024 that will close this issue
Add E gene trees #18
Closed
1 task
@j23414
Copy link
Contributor Author

j23414 commented Mar 14, 2024

Explore adding {gene}_coverage metadata columns for any gene/locus of interest using Nextclade, taking inspiration from the following RSV script:

@j23414 j23414 mentioned this issue Mar 22, 2024
Merged
1 task
@ammaraziz
Copy link

I'm that annoying user. Thank you so much for the E tree, it's been super helpful.

@j23414
Copy link
Contributor Author

j23414 commented May 8, 2024

Instead of documenting progress in individual PRs, e.g.

Posting the latest plan for the E gene workflow pipeline (so far) here:

pathogen-repo-guide (7)

@j23414 j23414 mentioned this issue May 8, 2024
Merged
3 tasks
j23414 added a commit that referenced this issue May 10, 2024
@j23414
E gene builds exclude the augur clades call
95a7ff3 
Until we have a set of E gene serotype and genotype defining mutations,
skip the augur clades call for E gene builds. This was originally discussed
for commit:

2f48ddb

Used in measles:

nextstrain/measles@ab92a1b

And diagrammed in:

#17 (comment)
j23414 added a commit that referenced this issue May 10, 2024
@j23414
E gene builds exclude the augur clades call
040d344 
Until we have a set of E gene serotype and genotype defining mutations,
skip the augur clades call for E gene builds. This was originally discussed
for commit:

2f48ddb

Used in measles:

nextstrain/measles@ab92a1b

And diagrammed in:

#17 (comment)
@j23414 j23414 mentioned this issue May 13, 2024
Merged
2 tasks
@j23414
Copy link
Contributor Author

j23414 commented May 23, 2024

Closed as completed since the following PRs are merged:

@j23414 j23414 closed this as completed May 23, 2024
@j23414 j23414 mentioned this issue May 29, 2024
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@j23414 j23414

Labels
enhancement New feature or request
Projects
None yet
Milestone
No milestone
3 participants
@j23414 @ammaraziz @joverlee521