I want to mine polymorphic SSRs between six varieties of a crop in order to employ them in MAS. I found the RAD PE sequences of these varieties are submitted to NCBI SRA. Can I use these RAD PE sequences to mine polymorphic SSRs? My plan is to align the RAD PE reads to the reference genome (variety wise) and then assemble the contigs. After this, these contigs derived from RAD PE of each variety will be used for identifying SSRs using tool such as MISA. After that, SSRs from all the six varieties will be compared to find polymorphic SSRs.
Is my approach worth to try or there may be better approach than this, please advise. Which software(s) or pipeline I can use for aligning the RAD PE reads to reference genome and assembly of the contigs. Thanks.