--fill-gaps eventually adds a furin cleavage site to everyone about avian-flu HOT 2 CLOSED

I think this is due to the default behavior of augur translate being to infer ambiguous nucleotides, and could be remedied by adding --keep-ambiguous to the ancestral rule.

from avian-flu.

Thanks for flagging this! This is definitely an error caused by the combination of --fill-gaps in augur align and not having --keep-ambiguous in augur translate. This has been fixed with this commit, which does a few things:

1. Removes --fill-gaps in augur align
2. Adds --keep-ambiguous in augur translate
3. Adds a new rule, rule cleavage-site, which reads in the HA alignment, translates it, and infers whether the 4 amino acids immediately preceding HA2 encode a furin cleavage motif. Here, I've defined a furin cleavage motif as the sequence R-X-K/R-R, where X is any amino acid. This results in 2 new colorby options: furin cleavage motif, which can be present or absent, and cleavage site sequence, which displays the sequence of the 4 amino acids immediately preceding HA2.

As expected, we now display that some high-path H5N1 and H5Nx lineages have furin cleavage sites, but that the vast majority of H9N2 and H7N9 sequences do not.

from avian-flu.