snippy
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reference in gbk/gb OR fasta+gtf/gff
I was using Snippy and I recommend the use of this software. Great Job! When I ran it with a reference in gbk file format Snippy split it into Fasta+GTF and then proceed, but there is not an option to use fasta+gtf as an input by default. It would be great to have this option as part of the main options.