i dont know software for genome sequencing. I havent done sequencing by myself, only worked with sequences but did not sequence myself. If you are new to it would be helpful to be familiar with databases, like EMBL nucleotide sequencing database or look around EBI website, google EMBL-EBI should come up with something. If you already have your genome u can start with multiple alignment use clustal x or w, use the latest one. You can also start by looking at genome browsers, you can find these online.
Satchi