Input files

[illusion-a]

Hello, I have some questions about the input file of snippy. Can snippy mix the draft genome and the fully assembled genome from Genebank as input files? I tried to put the draft genome and Complete genome (Scaffolds level and Complete genome) into a folder, and then used the snippy-multi command to obtain the core gene alignment of these strains to build the phylogenetic tree. Is the result obtained by this method reliable? Another question is if I change the reference gene sequence to the sequence of a gene cluster, also using snippy-multi, will I end up with a phylogenetic tree of that cluster across all strains? How do I know the total number of SNPS? Best wishes！