title: Illumina HiSeq of Staph aureus TX0117
design: Genomic DNA sequencing libraries were prepared using a miniaturized version of the Kapa HyperPlus Illumina-compatible library prep kit (Kapa Biosystems). DNAextracts were normalized to 5 ng total input per sample using an Echo 550 acoustic liquid handling robot(Labcyte Inc), and 1/10 scale enzymatic fragmentation, end-repair, and adapter-ligation reactions carried out using a Mosquito HTS liquid-handling robot (TTP Labtech Inc). Sequencing adapters were based on the iTru protocol (Glenn et al, 2016), in which short universal adapter stubs are ligated first and then sample-specific barcoded sequences added in a subsequent PCR step. Amplified and barcoded libraries were then quantified using a PicoGreen assay and pooled in approximately equimolar ratios before being sequenced on an IlluminaHiSeq 4000 instrument.