WORKSHOP: Long read sequencing for bacterial genomics

This record includes training materials associated with the Australian BioCommons workshop ‘Long read sequencing for bacterial genomics'. This workshop took place over two, 4 hour sessions on 7-8 October 2026.

Event description

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 introduces 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.

Lead trainers: 

• Dr Magdalena Antczak, Bioinformatician, QCIF Digital Research
• Dr Michael Geaghan, Sydney Informatics Hub (SIH), University of Sydney

Facilitators:

• Claire Herne, Bioinformatician, QCIF Digital Research

• Dr. Mitchell O'Brien, Senior Bioinformatics Engineer, Sydney Informatics Hub (SIH), University of Sydney

Infrastructure provision: 

• Dr. Mitchell O'Brian, Sydney Informatics Hub (SIH), University of Sydney
• Dr Giorgia Mori, Australian BioCommons

Coordination and host:

• Dr Giorgia Mori, Australian BioCommons

Files and materials included in this record:

• Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.

• Training materials including exercises: : https://sydney-informatics-hub.github.io/long-read-sequencing-workshop-2026/

This workshop follows materials collaboratively developed and maintained by QCIF (bioinformatics), Sydney Informatics Hub and the Australian BioCommons.