Easy reference-guided assembly of nanopore whole plasmid sequencing datasets

Whole plasmid sequencing (WPS) using Nanopore long read sequencing has emerged as a cost-effective alternative for dideoxy sequencing methods. De novo sequence assembly for large plasmids, however, are not always successful and may produce large assembly gaps. Here we streamlined a reference-guided alignment of WPS nanopore reads using galaxy platform. The process is straightforward and facilitate introduction of WPS as an alternative for researchers who are more used to dideoxy sequencing platform. We demonstrate that our procedure can assemble nanopore sequence reads with different quality datasets and identify variations from reference sequence.