Finding simple sequence repeat (SSR) markers for a specific disease

Question

[seta]

Hi all,

I have got Illumina sequencing reads from a healthy and diseased mouse. I want to compare the simple sequence repeats (SSR) between healthy and disease groups and discover the disease-related SSR markers. This is my first experience on this issue, so I was wondering what is the suitable pipeline for this work? any comment and suggestion would be highly appreciated.

Thanks