The advent and continual advancement of whole genome sequencing technology has dramatically improved our ability to investigate bacterial genomes at the highest possible resolution. However, despite their small size, many bacterial genomes are unable to be completely resolved using short-read sequencing alone. This is primarily due to the abundance of repetitive regions and mobile genetic elements in bacterial genomes, which often lead to collapsed repeats and ultimately breaks in the final assembly. This becomes problematic for downstream analyses, as these repetitive regions, which often contain important genomic features such as virulence or antibiotic resistance genes, cannot be accurately contextualised in the final assembly.
To overcome this problem, long-read sequencing technologies have been developed to span across repetitive regions and generate complete assemblies. Two of the main technologies currently offering long-read sequencing for bacterial genomes are Pacific Biosciences Single Molecule Real-Time (SMRT) sequencing, and Oxford Nanopore long-read sequencing. In this talk, I will discuss the advantages and disadvantages of both long-read sequencing technologies, and expand on the types of analyses we have used as well as those in the literature. This talk will focus on the application of long-read sequencing in microbial genomics and meta-genomics, with a particular focus on bacterial isolates in clinical settings.