***Sequenced using HiSeq
Sequences were assessed for Illumina adapter sequences in the 3’-end of the read using cutadapt v1.7.1 (parameters: -a AGATCGGAAGAGC -e 0.08 –overlap=3) (Martin 2011). Sequences were then trimmed based on quality scores using Trimmomactic v0.33 with a sliding window of 10bp and an average quality score cutoff of 28 (Bolger 2014). All sequences trimmed below 75bp in length were discarded (parameters: SLIDINGWINDOW:10:28 MINLEN:75). Only read pairs for which both mate survived trimming were retained for assembly and read coverage analysis.