Amplicons assembly/aligning method to find its targets?

[ezjung]

I am testing a cencer diagnostic panel which amplifies some of the cancer "Hot spots". Manufacturer did not provide the bed file for the targets. Primer sequence has been removed by UNG and nuclease and ends of the fragments all different.

I am thinking about finding the target for the amplicon by assembling/aligning the reads. What will be the most efficient way to do this? Can I use RNAseq assembler, like cufflinks or trinity? Seems like they are overkill for this purpose though.

Thanks in advance!