Entering edit mode
7.6 years ago
Hello there
I am a noob to WGS.
I am studying bacteria
The bug I am studying is quite variable
I sequenced some strains, assembled with SPADES and annotated with PROKKA.
I want to make snp calling based on the *.faa file. I want to use the amino acids and not the nucleic acid simply because the bacteria is very unstable genetically speaking and a snp call based on nucleic acid will probably return way too much snp that probably wont mean anything in tern of phylogeny.
I am trying to find tools and workflow that would allow that.
many thanks.