Hi

I have sequencing data [reads] from three strains of bacteria whose reference sequence is now known

• To obtain a reference sequence i do an assembly using all these data using velvet or MIRA3. My interest is to now find the SNPs in the non-repeat regions in each of these strains and hence i map my reads to this reference sequence. since i dont have reference sequence and no GTF/gff files, how do i get to know about SNPs in the non-repeat regions.
• If i get information about repeat regions using a detailed literature survey, do we have any component, which can write these regions in a GTF/GFF file format, so that it can be incorporated with the reference sequence