Add E gene builds

[j23414]

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

• Split by dengue serotype (denv1-denv4) #19
• Nextclade assignment #16

[joverlee521]

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

[j23414]

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

• rsv/ingest/bin/extend-metadata.py

[ammaraziz]

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

[j23414]

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

• Add gene coverage columns during ingest workflow #36

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

[j23414]

Closed as completed since the following PRs are merged:

• Generate gene reference files #47
• Use gene reference files to generate E gene trees #48