Open joverlee521 opened 1 week ago
Tracked down why we are currently using both MPXV and hMPXV Nextclade datasets in https://github.com/nextstrain/mpox/pull/114#discussion_r958185115:
align now uses hmpxv. shouldn't matter much in practice, but I think people will be more confidence when the alignment is based on an actual sequence, rather than a reconstructed ancestor.
Since the v3 Nextclade datasets for MPXV and hMPXV both use NC_063383.1 as the reference, we can just run Nextclade once using the MPXV dataset.
Migration to Nextclade v3 guide for reference.
Phylogenetic workflow was migrated in https://github.com/nextstrain/mpox/pull/245.
TODOs