PacBio WGS of Citrobacter braakii
DNA extracts were initially sheared to an average length of  15kb using g-tubes, as specified by the manufacturer (Covaris, Woburn, MA,  USA). Sheared DNA was used in SMRTbell library preparation, as recommended by  the manufacturer. Quantity and quality of the SMRTbell libraries were  evaluated using the High Sensitivity dsDNA kit and Qubit fluorometer and DNA  12000 kit on the 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). To obtain  the longest possible SMRTbell libraries for sequencing (as recommended by the  manufacturer), a further size selection step was performed using the PippinHT  pulsed-field gel electrophoresis system (Sage Science, Beverley, MA, USA),  enriching for the SMRTbell libraries >15kb for loading onto the  instrument. Sequencing primer and P6 polymerase were annealed and bound to  the SMRTbell libraries, and each library was sequenced using a single SMRT  cell on the PacBio RSII sequencing system with 240-minute movies.