title: Whole genome sequencing with Oxford Nanopore for Escherichia coli HUM3355
design: 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