Short read sequencing has long been a default choice for many genomics studies, given its high accuracy. However, the restricted read length of 150-300bp limits its usefulness for genome assembly, particularly when trying to resolve large repetitive elements. In the field of bacterial genomics, accurate and complete genome assembly is key to distinguishing between genes present on the main chromosome versus mobile plasmids, which influence how elements like antimicrobial resistance genes spread.
The adoption of long read sequencing, with its multi-kilobase read length, has quickly risen in recent years to address these limitations. However, long read sequencing, particularly within the context of bacterial genomics, has its own set of challenges that require careful consideration.
This workshop will introduce you to the fundamentals of long read sequencing and how it can be used to assemble and analyse bacterial genomes. You will be guided through standard quality control analysis and pre-processing of long read sequencing data, assembling a bacterial genome, identifying plasmids, and annotating the genome to identify antimicrobial resistance genes of importance to hospital-acquired infections.
Participants trained: 24
Citation
Antczak M, Geaghan M, Herne C, O’Brien MJ. WORKSHOP: Long read sequencing for bacterial genomics. Zenodo. https://doi.org/10.5281/zenodo.23327650