Add phylogenetic - Githubissues

nextstrain / lassa

Nextstrain build for Lassa virus

https://nextstrain.org/staging/lassa

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Add phylogenetic #8

Closed j23414 closed 3 months ago

j23414 commented 4 months ago

Description of proposed changes

Add phylogenetic workflow

Refactor workflow into a phylogenetic directory to match pathogen repo guide
Pull curated NCBI genbank data from s3 instead of Fauna
Since original trees were built from S and L segments, add rules and configs to pull out segments from NCBI GenBank sequences using Nextclade
Update phylogenetic automation rules

The resulting phylogenetic trees are staged at:

Related issue(s)

Checklist

[ ] Checks pass

Post-merge clean up

As mentioned in https://github.com/nextstrain/conda-base/pull/85#discussion_r1683286635, once this is merged, various downstream CIs will need to be updated:

j23414 commented 3 months ago

This additional commit (https://github.com/nextstrain/lassa/pull/8/commits/7cde2593eb58fe66e8995dd6a7173dfc1f810721) updates augur filter to allow visualization of all S (694) and L (1272) segments in Auspice, following @jameshadfield's suggestion during a call.

I removed some group-by filtering to include more data while adding a minimum length filter to ensure quality. This change enables a comprehensive view of the dataset.