Project title
Accelerating nanopore basecalling on different GPU architectures
Collaborators and funding
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School of Computer Science and Engineering, UNSW Sydney https://www.unsw.edu.au/engineering/our-schools/computer-science-and-engineering
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Genomic Technologies Lab, Garvan Institute of Medical Research https://www.garvan.org.au/research/labs-groups/genomic-technologies-lab
Contact(s)
- Hasindu Gamaarachchi, UNSW Sydney, hasindu@unsw.edu.au
Project description and aims
Nanopore is a leading third-generation long-read sequencing technology that can sequence native DNA and RNA molecules. The output of nanopore sequencers is a current signal measurement, which is converted to nucleotide bases using a process known as basecalling. Basecalling of nanopore sequencing data from raw current signals to nucleotide bases is a computationally demanding process that often relies on neural-network inference on GPUs.
In this project, we expect support and then accelerate the basecalling process on multiple GPU architectures from different vendors, including the AMD GPUs that are available in the Pawsey supercomputer. https://github.com/BonsonW/slorado
How is ABLeS supporting this work?
This work is supported through the software accelerator scheme provided by ABLeS. The supports includes 1 TB long term storage and 20 KSUs per quarter.
Expected outputs enabled by participation in ABLeS
An opensource basecaller that can perform basecalling on multiple different GPU architectures. There could also be preprints or publications, depending on the success of this project.
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.