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: Request to add a GPC Phylogenetic Tree  #20

Checklist

• Checks pass

[j23414]

Thanks! I see you're using the Josiah reference which matches 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 (Pinneo-NIG-1969)
• 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.

[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. — Reply to this email directly, view it on GitHub <#21 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOVPUJTOIOLU3RF64AXVM53ZQOEPPAVCNFSM6AAAAABME6DYSKVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDEMRYGIYTSMZZG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>