Hi there! 
I was looking into augur translate code to learn how Nextstrain translates gapped or partially gapped aligned sequences such as A-- codon.
Apparently it is translated as ‘X’ and not as frameshift. What is the explanation for that?
Thank you,
Dana.
Hi Dana,
augur translate translates a sequence codon by codon. Incomplete codons are translated as X, while --- codons are translated as -. We will soon deploy an alternative translation for the SARS-CoV-2 analyses that translates the actual coding sequence independent of its alignment at the nucleotide level. However, small deletions that are the result of sequencing errors will then mess up the entire protein.
best,
richard