Enriched Array Fragment Assembly

All 5′ fragments were amplified off the array using HSSF-ATGC and DO_15R_PU (Supplemental Table 8) with KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit (Kapa Biosystems) and stopped before plateauing. All 3′ fragments were amplified off the array using DO_5F_PU and HSS-95R (Supplemental Table 8). Both were purified using a 1.8x AMPure cleanup and eluted in 20 μL Qiagen EB. 2 μL of USER enzyme (NEB) was added directly to each purified PCR product, and incubated for 15 minutes at 37 °C followed by 15 minutes at room temperature. Reactions were then treated with the NEBNext End Repair Module (NEB) following the manufacturer’s protocol, and purified using the DNA Clean and Concentrator 5 (Zymo Research) and eluted in 12 μL EB, following the manufacturer’s protocol. We then quantified DNA concentrations for both treated samples using a Qubit and diluted samples to 0.75 ng/uL. We then assembled the 5′ and 3′ fragments as described previously^{25 (link)}. Briefly, fragments were allowed to anneal and extend for 5 cycles with KAPA HiFi 2X HotStart Readymix (Kapa Biosystems) before primers HSSF-ATGC and DO_95R were added for amplification (Supplemental Table 8).