Ultra-long Nanopore sequencing of Bordetella pertussis

A Bordetella pertussis isolate (UK54) was predicted to have a Copy number variant aprroximately 16kb long with a copy number of 4- a tandem length of 64kb. In order to resolve these mutations, ultra long nanopore reads were generated (protocol: https://www.protocols.io/view/ultra-long-read-sequencing-protocol-for-rad004-mrxc57n). We generated datasets with very long reads. Sequencing the UK54 original stock and two clones revealed that in two out of three samples whole tandem arrays of CNVs could be isolated. Within these samples, there were arrays with different copy numbers which therefore indicates that rapidly segregating populations of cells were being sequenced.