Overview of IS-seq Method. Genomic DNA (gDNA) is randomly sheared and ligated to adapters containing 24 different barcodes (BC, purple circles). Amplification from the IS 6110 ends is done in a first PCR (PCR1) with primers that anneal on the IS 6110 (blue) and the adapter (green), incorporating additional BC (yellow circles) and the PE-sequencing primer (red). A second PCR (PCR2) is done to incorporate amplification primers (orange and light blue). Sequencing is carried out using regular PE-primers in an Illumina-GA II.