Project title
Genomics in a Backpack: A portable genomics workflow for pond side sequencing of bacterial pathogens for sustainable aquaculture
Collaborators and funding
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Sydney School of Veterinary Sciences, University of Sydney
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Sydney Institute for Infectious Diseases, University of Sydney
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Sydney Informatics Hub, University of Sydney
Funded by Sydney Institute for Infectious Diseases 2023 Seed Funding.
Contact(s)
- Project co-lead: Dr Francisca Samsing Pedrals francisca.samsingpedrals@sydney.edu.au
- Project co-lead: Dr Carola Venturini carola.venturini@sydney.edu.au
- Bioinformatics lead: Dr Georgie Samaha georgina.samaha@sydney.edu.au
Project description and aims
Marine Vibrios have been labelled the microbial barometer of climate change. Infections with this opportunistic pathogen are increasing globally with ocean warming and the intensification of aquaculture. Positioned downstream of terrestrial aquaculture and urban environments, marine aquaculture systems are major reservoirs of antimicrobial resistance. Limited access to on site genomic testing is a significant challenge facing the Australian marine aquaculture industry. The conventional workflow for whole genome sequencing demands both capital investment and expertise, relying on technologies that are scarcely available remotely.
This project aims to address this bottleneck by developing an automated whole genome sequencing and analysis workflow for bacterial isolates sequenced using Oxford Nanopore sequencing data pond-side.
How is ABLeS supporting this work?
This work is supported through the production bioinformatics scheme provided by ABLeS. The support includes 1 TB temporary storage on scratch and 10 KSUs per quarter.
Expected outputs enabled by participation in ABLeS
A public scalable computational workflow for bacterial genome assembly and genetic profiling that can be deployed across national HPC facilities and commercial cloud.
These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.