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Sidharth Maheshwari

Implementing computational pipelines of whole genome sequencing on embedded platforms.

Email: s.maheshwari2@ncl.ac.uk

Supervisors

Project description

I am implementing computational pipelines of whole genome sequencing on embedded platforms. The implementation will be energy-efficient and performance-driven.

We have designed an OpenCL-based read mapping tool for assembling genome. The tool uses a read alignment approach. Focus is on designing low-footprint performance optimised kernels for cross-platform implementation. The implementation targets modern heterogeneous architectures on:

  • general purpose computers
  • embedded system-on-chip (SoC)
  • Field Programmable Gate Arrays (FPGA)

Our experiments show significant energy savings along with improved performance and accuracy.

We have demonstrated a working prototype of embedded genomics. We used a HiKey 970 Embedded SoC using ARM Big-Little technology. The results show enhanced energy savings compared to general purpose computers. Performance and accuracy were similar. We have compared our proposed tools with state-of-the-art read mappers to validate accuracy.

We are working towards assembling the entire human genome on memory-limited embedded SoC. This would provide low energy and low cost genomics.

We are also working on an OpenCL-based FPGA implementation of genomic kernels. This will provide a wholistic comparison of all available hardware platforms. It will enable us to determine optimal hardware solutions to genome assembly. For low-power high performance genomics, we are exploring dedicated Embedded SoC clusters.

Publications

  • Maheshwari S, Gudur VY, Shafik R, Wilson I, Yakovlev A, Acharyya A. CORAL: Verification-aware OpenCL based Read Mapper for Heterogeneous Systems. In: IEEE/ACM Transactions on Computational Biology and Bioinformatics 2019. doi: 10.1109/TCBB.2019.2943856
  • Maheshwari S, Shafik R, Yakovlev A, Wilson I, Acharyya A. REPUTE: An OpenCL based Read Mapping Tool for Embedded Genomics. 2020 Design, Automation & Test in Europe Conference & Exhibition, Alpexpo, 2020.

Interests

  • Bioinformatics
  • Biomedical Engineering
  • Energy-efficient Hardware Solutions for Healthcare Applications
  • Embedded SoCs
  • VLSI Architectures

Qualifications

Bachelor of Technology, Electrical and Electronics Engineering, Indian Institute of Technology (IIT) Guwahati

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