genome comparisons-identifying unique sequences

[NGS_New_User]

Hi everyone,

I have assembled de novo the genome of a non model organism, whose female has two strains. My goal is to identify unique sequences between the two types of females. That is to extract information that will show the uniqueness/variation/difference between the two. I have the raw illumina PE 100 bp reads of both, the assembled genomes of both flies, the predicted proteins from each genome, and a recent assembled transcriptome of this organism.
So, my question is, how can I effectively extract the unique sequences from these two strains. What pipeline can anyone advise me to follow, and what programs to use?
I will sincerely appreciate any suggestions and ideas.
Thanks in advance

[westerman]

As a first pass I wouldd use Mummer to align the genomes. This assumes that the genomes are more-or-less fully assembled.