Whole genome sequencing with Oxford Nanopore for Klebsiella pneumoniae HUM7199
To extract genomic DNA, cells were lysed by boiling with detergent, followed by ethanol precipitation of DNA as previously described in [DOI: 10.3389/fmicb.2018.01894]. For long-read sequencing, the DNA was sheared using g-TUBEs (Covaris, Massachusetts) to obtain fragments averaging around 8 kbp in length following the manufacturers protocol. Long-read library preparation was done with the SQK-LSK109 ligation sequencing kit and the EXP-NBD103 native barcoding expansion kit (Oxford Nanopore Technologies). Libraries were sequenced on a MinION R9.4.1 flow cell and reads were basecalled and demultiplexed with Guppy v4.2.2