title: All WGS libraries for E. macaco sample Harmonia (source for reference-based E. macaco assembly)
design: PE libraries with mean target insert size of 500 bp were prepared with Illumina’s TruSeq DNaseq Sample prep kit at the Keck Sequencing Center of the University of Illinois (Champaign, IL); these libraries were also sequenced at the Keck Center. PE libraries were quantitated by qPCR and sequenced for 100 cycles from each end of the fragments on a HiSeq2000 machine using a TruSeq SBS sequencing kit version 3. Reads were analyzed with Casava 1.8 (pipeline 1.9) and subsequently stripped of adaptors. Duplicates were marked using Picard MarkDuplicates, and reads were mapped using used the recommended pipeline within BWA version 0.5.9 and locally around indels using GATK’s RealignerTargetCreator and IndelRealigner.