Preparation of fragmented PhiX174 DNA
The sequencing libraries were prepared using PCR-free kits from 200 ng of fragmented PhiX174 DNA. For the fragmentation, 1.5 µg of PhiX174 RF II DNA (NEB, Ipswich, MA) was diluted in a final volume of 100 µL TE 10:1 in 0.5 mL Bioruptor microtubes and sonicated using Bioruptor UCD-200 (Diagenode, Seraing, Belgium) at LOW power (160 W) during 12 pulses of 30s ON/90s OFF. A buffer exchange was performed with 10 mL Tris-HCl pH8.0 using the kit NucleoSpin Gel and PCR Clean-up (Macherey-Nagel, Düren, Germany). The profile of the fragmented PhiX DNA was controlled on the Agilent Bioanalyzer 2100 instrument using the High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA), and the average fragment size was determined to be 289 bp. DNA was quantified using the Qubit 1X dsDNA High Sensitivity Assay kit (ThermoFisher Scientific, Waltham, MA) before library preparation.