Pawsey enables more flexible and scalable DNA analysis
This story about researchers accessing high performance computing via the Australian BioCommons Leadership Share (ABLeS) was first published by the Pawsey Supercomputing Research Centre.
Dr Hasindu Gamaarachchi and Bonson Wong, the researchers behind Slorado, the new open source software for nanopore sequencing basecalling on AMD GPUs. Credits UNSW Sydney
Researchers from UNSW Sydney and the Garvan Institute of Medical Research have developed Slorado, the first open-source software/library solution for nanopore sequencing basecalling on AMD Graphic Processing Units (GPUs). Using Setonix, Australia’s most powerful supercomputer at the Pawsey Supercomputing Research Centre, this development enables researchers worldwide to process nanopore sequencing data on any mainstream GPU hardware for the first time, expanding computational options for the global bioinformatics community.
Oxford Nanopore Technologies (ONT) sequencers generate time-series raw signals that need to be converted into DNA bases through a process called basecalling. While ONT’s Dorado software supports NVIDIA GPUs for this process, AMD GPUs are currently not supported.
Led by Dr Hasindu Gamaarachchi and PhD candidate Bonson Wong, the team has created a streamlined version of the industry-standard Dorado basecaller that removes previous hardware limitations while maintaining and in some cases increasing performance. This innovation allows researchers to utilise AMD GPUs, including those in Pawsey’s Setonix, Australia’s fastest and most energy-efficient research supercomputer, reducing processing times and wait periods for critical genomic research.
Pawsey CEO Mark Stickells underscored the impact of this development:
“Dr Gamaarachchi’s work highlights our mission to accelerate scientific discovery. Fast, efficient bioinformatics is key to addressing challenges in medicine and biotechnology, from genomic analysis to drug discovery and personalised medicine. By enabling nanopore sequencing on Setonix’s AMD GPUs, we are breaking down computational barriers and empowering researchers with world-class tools,” Mark said.
“This collaboration demonstrates how state-of-the-art infrastructure can transform research workflows and broaden access to advanced computational tools.” He continued.
Dr Gamaarachchi and Bonson Wong shared their vision for Slorado:
”Our goal was to expand computational options for the bioinformatics community. By enabling basecalling on AMD GPUs and making the software fully open-source, we are empowering researchers to process their data more efficiently using both AMD and NVIDIA hardware.”
Slorado supports up to eight GPUs simultaneously on the same node, delivering unprecedented processing capabilities when combined with systems like Setonix. Researchers can now achieve faster results without enduring lengthy queue times, accelerating the pace of critical genomic discoveries.
The team access to Setonix has been supported via the Australian BioCommons Leadership Share (ABLeS).
To know more about Slorado, register for an online event on 18 Mar 2025:
Accelerating Nanopore Analysis: Introducing the new Open Source Slorado.