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.
Learning outcomes:
By the end of the workshop you should be able to:
Explain the fundamentals of long read sequencing, how it differs from short read sequencing
Assess long read sequencing run and read quality using standard quality control tools
Construct de novo bacterial genome assemblies from ONT long read sequencing data and assess genome quality
Annotate, analyse, and compare assembled genomes to identify antimicrobial resistance genes and sequence similarities between samples
Lead Trainers:
Dr Magdalena Antczak, Bioinformatician, Queensland Cyber Infrastructure Foundation (QCIF)
Dr Michael Geaghan, Senior Bioinformatician, Sydney Informatics Hub, The University of Sydney
Date/Time: 7-8 October 2026, 12 - 4 pm AEST / 11:30 am - 3:30 pm ACST / 10 am - 2 pm AWST (Check in your timezone)
Location: Online
Format: This online workshop will take place over two four-hour sessions. You must attend both sessions in order to get the most out of the workshop. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action.
Who the workshop is for:
This workshop is for Australian researchers in academia, government or industry who have or will work with long read sequencing for bacterial genomics as part of their projects. You must be associated with an Australian organisation for your application to be considered.
Prerequisites
Prior experience working in a Linux command-line environment, including navigating Unix-style file systems, executing commands, and writing scripts.
How to apply:
This workshop is free but participation is subject to application with selection.
Applications close at 11:59 pm AEST, Tuesday 29 September 2026.
Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. More information on the selection process is provided in our Advice on applying for Australian BioCommons workshops.
This workshop is presented by Australian BioCommons, Sydney Informatics Hub and QCIF, with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to the Australian BioCommons newsletter