Illumina sequencing of HiBC strain CLA-JM-H17
Library preparation and sequencing were conducted using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina with dual index primers and 300ng of DNA (NEB Inc.) on an automation platform (Biomeki5, Beckman Coulter) according to the manufacturers instructions. The time used for enzymatic shearing to ca. 500bp to be used on a MiSeq run was 10min, and to ca. 200bp to be used on a NextSeq run was 30min. PCR enrichment of adaptor-ligated DNA was conducted with five cycles using NEBNext Multiplex Oligos for Illumina (NEB, USA) for paired-end barcoding. AMPure beads (Beckman Coulter, USA) were used for size selection and clean-up of adaptor-ligated DNA. Sequencing was performed either at the IZKF Core Facility Genomics (Uniklinik RWTH Aachen) on a NextSeq platform (Illumina) (PE 150bp) or on a MiSeq (Illumina) (PE 300bp) in-house