Use nextalign instead of custom Python codon alignment script about seasonal-flu HOT 3 CLOSED

Now that Nextclade has seasonal flu datasets, we should consider using Nextclade for alignment and clade annotations in our standard builds. This approach would quickly produce codon-aware nucleotide alignments, amino acid translations, and clade annotations for every sequence in the database.

from seasonal-flu.

We'll need to setup the corresponding FASTA reference files for all of the lineages and segments

For the Nextalign part, there are many input files in Nextclade repo already. You'll probably need something even more sophisticated that that. But this might be a partial solution ar at least a starting point:

https://github.com/nextstrain/nextclade/tree/master/data/flu

We should consider using Nextclade for alignment and clade annotations in our standard builds

Nextclade would require more files to run than Nextalign, including a reference auspice tree for every variation, every root sequence etc. So much more involved in terms of science things. Unless it all can piggyback on the existing trees somehow:

https://github.com/nextstrain/nextclade_data/tree/master/data/datasets

In either case, happy to help with the engineering part! Sadly I am almost entirely ignorant about the science of flu itself.

from seasonal-flu.

Closing this since we've used nextalign since the refactor.

from seasonal-flu.