Annotate sequences for upload to ENA and for download by user

[rneher]

We translate genes and report amino acid mutations, but we don't relay the coordinates of the features to ENA (NCBI wouldn't allow that). Hence sequences we submit look "draft-y" on genbank. Since we have this information, we should make this information available to INSDC. We could also allow users to download annotated genomes, e.g. via a GFF3 or genbank file.

[theosanderson]

(all agreed with the general idea of this issue)

Since we have this information

I'm not sure to what extent we currently have this information stored in a format useful for INSDC, or indeed for potentially displaying it ourselves (e.g. with Gensplore which is available as a react component). Below I start thinking about this:

As I understand it what we store is:

• Unaligned genome
• Nucleotide sequences hard-aligned to reference sequence
• Amino acids hard-aligned to reference sequence
• Lists of insertions and deletions, both for amino acids and nucleotides
• We also have, in the Nextclade dataset, the coordinates for feature locations in the reference genome

What we need for INSDC is:

• an unaligned genome (which we have)
• a list of coordinates for various features in that genome. We don't have this to hand. But I guess we can maybe compute it by applying the list of nucleotide insertions and deletions to the coordinates in the reference genome?
• likely to calculate unaligned amino acid translations, based on these coordinates.