Illumina HiSeq 2000 sequencing
The library preparation protocol is detailed in (Rowan et al, 2017). Briefly, DNA was digested and then ligated to barcoded adapter sequences with sticky ends complementary to the KpnI cleavage site. After ligation, 96 barcoded samples were pooled and then sheared using the Covaris S220 instrument (Covaris, Woburn, MA). Next, end-repair, dA-tailing, a second universal adapter ligation, and PCR enrichment were performed using the Illumina compatible NEBNext DNA Library Prep Master Mix Set (NEB, Ipswich, MA).