Researchers come together to tackle the bioinformatics of fungal genomics

A collage of photos show a large group of people talking in a classroom setting and watching speakers make presentations, overlayed with logos of Australian Functional Biology, Bioplatforms Australia and The Plant Pathogen Omics Initiative.

Bioplatforms Australia brought together members of the Functional Fungi and Plant Pathogen Omics National Initiatives for a hands-on fungi bioinformatics workshop. Recognising that high throughput sequencing is the new normal for fungi research, hosts A/Prof Benjamin Schwessinger (Australian National University) and Dr Alistair McTaggart (Psymbiotika Lab) guided 38 researchers through theory sessions, hands-on practice, and real examples of applying bioinformatics to fungal research. Attendees were of diverse backgrounds  in commercial enterprise, academia, government research and citizen science.

Each theory session was followed by a hands-on demonstration using Galaxy Australia. For example, Dr Mareike Möller (ANU) led a theory session on fungal genome assembly covering key concepts such as why long reads are essential for assembling complete genomes, and why genome assembly is like tackling the world’s hardest jigsaw puzzle. This was followed by Dr Anna Syme’s demonstration of genome assembly on Galaxy Australia. Anna wrote six dedicated workflows for fungi, which are now publicly available for any Australian to reuse or adapt on Galaxy Australia. To access them, head to Public Workflows and filter by tag ‘fungi’. If you’re just getting started with workflows, watch Anna’s Top Tips for using Galaxy workflows.

Benjamin and Alistair ensured the workshop was directly relevant to real-world fungal and plant pathogen research. All demonstrations used fungi data shared by Alistair, plus Dr Tara Garrad and Dr Kelly Hill from the South Australian Research and Development Institute, which remains available in the Bioplatforms Australia Data Portal.

Workshop participants felt that the mix of hands-on and theory sessions was ideal; demystifying the technology and bringing clarity to the broad array of options available in Galaxy Australia. Workshop materials and metadata are available in the Australian BioCommons Training Materials Zenodo repository.

Christina Hall2024