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participants/nanopore.md

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+---
+title: School of Computer Science and Engineering, UNSW Sydney.
+description: The project aims to first support and then accelerate nanopore basecalling on multiple
+GPU architectures from different vendors.
+toc: false
+type: ABLeS Participant
+---
+
+## Project title
+Accelerating nanopore basecalling on different GPU architectures
+
+## Collaborators and funding
+
+- School of Computer Science and Engineering, UNSW Sydney [https://www.unsw.edu.au/engineering/our-schools/computer-science-and-engineering](https://www.unsw.edu.au/engineering/our-schools/computer-science-and-engineering)
+
+- Genomic Technologies Lab, Garvan Institute of Medical Research [https://www.garvan.org.au/research/labs-groups/genomic-technologies-lab](https://www.garvan.org.au/research/labs-groups/genomic-technologies-lab)
+
+## Contact(s)
+
+- Hasindu Gamaarachchi, UNSW Sydney, <[email protected]>
+
+
+## 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.
+
+<br/>
+
+> *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.*