Nanopore sequencing based cgMLST for GC rich pathogens like Burkholderia pseudomallei

Whole genome sequencing (WGS)-based pathogen surveillance allows the in-depth analysis of phylogenetic relationships and the exploration of virulence and resistance markers. Currently its application is limited by poor cost-efficiency due to reliance on short read (SR) sequencing. This could be massively improved by applying Oxford nanopore long read (ONT-LR) sequencing instead. We challenge this approach using the pathogen Burkholderia pseudomallei, which possesses one of the most complex bacterial genomes with 68% GC content and validate it against native library preparation in combination with state-of-the art data processing tools.