Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5' end (-trim_left 10), trim reads with low quality on the 3' end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65).  We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore  (--stringency 1).
