No, you do not require SFF files. If you have SFF files, the first step is to convert to Fasta, qual and traceinfo files. As you have Fasta and qual files, you should be able to skip this step. However, you may need a traceinfo file (or equivalent) to inform mira3 about parameters such as strain name and library insert sizes. The manual contains details of how to make a traceinfo file by hand, if you do not have one.