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nextstrain / lassa

Nextstrain build for Lassa virus
https://nextstrain.org/staging/lassa
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Update references to match RefSeq #23

Closed j23414 closed 3 months ago

j23414 commented 3 months ago

Description of proposed changes

Switch to the RefSeq reference 'Josiah' for consistency.

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j23414 commented 3 months ago

Hmm, realizing that updating the references in phylogenetic triggers concurrent changes to segment references for ingest

j23414 commented 3 months ago

I've moved the updating segment reference files to a separate issue. The main changes in this PR are from this slack thread:

  1. Add Pinneo as explicit root
  2. Update reference to be Josiah

Which results in the following trees:

trvrb commented 3 months ago

Thanks for putting this together @j23414. In the above I just passed in two tips instead to specify a clade to root to. This isn't perfect, but is a bit less funky than TreeTime's behavior of placing root exactly on the specified tip.

Also, I added include.txt to make sure to always include these strains.

You can see resulting output here:

trvrb commented 3 months ago

@j23414: Could you add MG812675 to the example data? This should make the CI complete.

j23414 commented 3 months ago

Thanks @trvrb! I was wondering how to get a more reasonable root of the trees

I've updated the example data in https://github.com/nextstrain/lassa/pull/23/commits/6405c92408284da61ab4be3d8183bc754e33221c