Libraries were quantified between the range of 200bp and 1 kbp on a High Sensitivity Bioanalyzer kit (Agilent, Cat. 5067-4626). Libraries were sequenced on an Illumina NextSeq® 500 loaded at 0.8 pM with a custom sequencing chemistry protocol (Read 1: 50 imaged cycles; Index Read 1: 8 imaged cycles, 27 dark cycles, 10 imaged cycles; Index Read 2: 8 imaged cycles, 21 dark cycles, 10 imaged cycles; Read 2: 50 imaged cycles) using custom sequencing primers described in Amini et. al. 2015, Ref.14 (link). QRP and DOP libraries were sequenced using standard primers on the NextSeq® 500 using high-capacity 75 cycle kits with dual-indexing. For QRP there is an additional challenge that the first 15 bp of the read are highly enriched for “G” bases, which are non-fluorescent with the NextSeq® 2-color chemistry and therefore cluster identification on the instrument fails. We therefore sequenced the libraries using a custom sequencing protocol that skips this region (Read 1: 15 dark cycles, 50 imaged cycles; Index Read 1: 10 imaged cycles; Index Read 2: 10 imaged cycles).