In-silico enrichment of bacterial plasmids by chromosomal depletion using nanopore adaptive sampling

Adaptive sampling is an in-silico enrichment method unique to nanopore sequencing. Several studies have shown the potential to enrich low abundant sequences by rejecting unwanted molecules. Here, we assessed this approach for the enrichment of low abundant plasmids in known bacterial isolates using twodifferent adaptive sampling tools. We show that enrichment of 1.1-1.8x can be achieved even on reused or expired flow cells. Our experiments indicate that the choice of the read classification method and read lengths used for the classification influence the enrichment factor. By applying adaptive sampling, wealso improve the quality of de novo plasmid assemblies and reduce the sequencing time.