constructing a supercontig from selected reads

Question

[shynilasanthi]

I have illumina paired end RADseq dataset of two woodpecker species and their hybrids.I'm trying to make a hybrid index for the two species. for that I need to construct a supercontig using some selected reads from parental samples contain unique SNPs. Is there anyway to do that?because in the next step I have to use this supercontig as the reference to map the reads from all the samples.