An FPGA based Energy-Efficient Read Mapper with Parallel Filtering and in-situ Verification

Gudur, V. and Maheshwari, S. and Acharyya, A. et al. (2021) An FPGA based Energy-Efficient Read Mapper with Parallel Filtering and in-situ Verification. EEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). p. 1. ISSN 15455963

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In the assembly pipeline of Whole Genome Sequencing (WGS), read mapping is a widely used method to re-assemble the genome. It employs approximate string matching and dynamic programming-based algorithms on a large volume of data and associated structures, making it a computationally intensive process. Currently, the state-of-the-art data centers for genome sequencing incur substantial setup and energy costs for maintaining hardware, data storage and cooling systems. To enable low-cost genomics, we propose an energy-efficient architectural methodology for read mapping using a single system-on-chip (SoC) platform. The proposed methodology is based on the q-gram lemma and designed using a novel architecture for filtering and verification. The filtering algorithm is designed using a parallel sorted q-gram lemma based method for the first time, and it is complemented by an in-situ verification routine using parallel Myers bit-vector algorithm. We have implemented our design on the Zynq Ultrascale+ XCZU9EG MPSoC platform. It is then extensively validated using real genomic data to demonstrate up to 7.8 energy reduction and up to 13.3 less resource utilization when compared with the state-of-the-art software and hardware approaches.

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IITH Creators:
IITH CreatorsORCiD
Acharyya, Amit
Item Type: Article
Uncontrolled Keywords: Bioinformatics, Field programmable gate array, Field programmable gate arrays, filtering, Filtering, genome sequencing, Genomics, Hardware, low-cost, low-energy, read mapping, Sequential analysis, Software, verification
Subjects: Electrical Engineering
Divisions: Department of Electrical Engineering
Depositing User: Mrs Haseena VKKM
Date Deposited: 15 Nov 2021 05:18
Last Modified: 04 Mar 2022 07:15
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