Hi all,
We have sequenced a Bacteria on Ion PGM platform for Denovo sequencing. We did get a good scaffold data.

Our next aim is to take this as a reference sequence and compare it with remaining samples which were also sequenced on IonPGM.

Now do i have to order the contigs or scaffolds and then go for SNP search?
What are the tools which can be used for SNP predictions from draft genomes?
How do we annotate these SNP's?

Thanks in advance,