Adds required GPC references

[JoiRichi]

Description of proposed changes

For creating GPC trees, this PR adds the required GPC reference files.

Related issue(s)

• Related to: https://github.com/nextstrain/lassa/issues/20

Checklist

• [ ] Checks pass

[j23414]

I think we can ignore this check. I kicked it off to see what would happen on an external PR.

[JoiRichi]

Great!

The Josiah is the widely recognized reference in the field. I agree it should be used for the segments as well. This would ensure "universally comparable results".

On Thu, 8 Aug 2024, 17:23 Jennifer Chang, @.***> wrote:

@.**** approved this pull request.

Thanks! I see you're using the Josiah reference which matches RefSeq https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Mammarenavirus%20lassaense,%20taxid:3052310&SourceDB_s=RefSeq and seems good to me.

This does does make me wonder if we should swap our current L and S segment references to Josiah for consistency. Currently they are:

• lassa_l.gb https://github.com/nextstrain/lassa/blob/da8019bfe93e22bc7d12b683076f6e7ea5302df3/phylogenetic/defaults/lassa_l.gb (Pinneo-NIG-1969)
• lassa_s.gb https://github.com/nextstrain/lassa/blob/da8019bfe93e22bc7d12b683076f6e7ea5302df3/phylogenetic/defaults/lassa_s.gb (Nig08_04)

But that's a separate issue and PR. If I don't see other comments, I'll go ahead and merge this at the end of the week.

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