Illumina Amplicon NGS
PCR primers for loci of interest were designed using Primer3.  Adaptors were included in the primers for a second PCR reaction to add the Illumina library sequences (ACACGACGCTCTTCCGATCT forward primer and GACGTGTGCTCTTCCGAT reverse primer).  Regions of interest were amplified via PCR and purified.  A second PCR reaction was then performed to add sample specific sequence barcodes.  PCR libraries were purified and samples run according to manufacturers instructions.  Forward and reverse reads were merged with SeqPrep.  Reads were then demultiplexed followed by application of quality and amplicon filters.