I am working with whole genome sequences of bacteria and want to identify SNPs from the genomes for each sequences. What would be the best way to identify these SNPs that will allow me to compare the variation between them.
Thanks a lot.
If you are working with deep sequencing data, then I recommend following the short-read aligner suggestion described by Frederic Bigey.
If you are working with whole genome sequences (from NCBI Nucleotide, for example), I think base-by-base might be able to help you call the SNPs (which you can then interpret as GANI has suggested). I've used it to compare with viral genome sequences. Don't know what is the maximum allowed genome size, but you can check it out: