AlignS: A Processing-In-Memory Accelerator for DNA Short Read Alignment Leveraging SOT-MRAM

Classified as a complex big data analytics problem, DNA short read alignment serves as a major sequential bottleneck to massive amounts of data generated by next-generation sequencing platforms. With Von-Neumann computing architectures struggling to address such computationally-expensive and memory-...

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Published in:Proceedings of the 56th Annual Design Automation Conference 2019 pp. 1 - 6
Main Authors: Angizi, Shaahin, Sun, Jiao, Zhang, Wei, Fan, Deliang
Format: Conference Proceeding
Language:English
Published: ACM 01.06.2019
Subjects:
Bioinformatics
Computer architecture
DNA
Genomics
Magnetic tunneling
Micromechanical devices
Sequential analysis
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Abstract Classified as a complex big data analytics problem, DNA short read alignment serves as a major sequential bottleneck to massive amounts of data generated by next-generation sequencing platforms. With Von-Neumann computing architectures struggling to address such computationally-expensive and memory-intensive task today, Processing-in-Memory (PIM) platforms are gaining growing interests. In this paper, an energy-efficient and parallel PIM accelerator (AlignS) is proposed to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm. We first develop AlignS's platform that harnesses SOT-MRAM as computational memory and transforms it to a fundamental processing unit for short read alignment. Accordingly, we present a novel, customized, highly parallel read alignment algorithm that only seeks the proposed simple and parallel in-memory operations (i.e. comparisons and additions). AlignS is then optimized through a new correlated data partitioning and mapping methodology that allows local storage and processing of DNA sequence to fully exploit the algorithm-level's parallelism, and to accelerate both exact and inexact matches. The device-to-architecture co-simulation results show that AlignS improves the short read alignment throughput per Watt per mm 2 by ~12× compared to the ASIC accelerator. Compared to recent FM-index-based ReRAM platform, AlignS achieves 1.6× higher throughput per Watt.
AbstractList Classified as a complex big data analytics problem, DNA short read alignment serves as a major sequential bottleneck to massive amounts of data generated by next-generation sequencing platforms. With Von-Neumann computing architectures struggling to address such computationally-expensive and memory-intensive task today, Processing-in-Memory (PIM) platforms are gaining growing interests. In this paper, an energy-efficient and parallel PIM accelerator (AlignS) is proposed to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm. We first develop AlignS's platform that harnesses SOT-MRAM as computational memory and transforms it to a fundamental processing unit for short read alignment. Accordingly, we present a novel, customized, highly parallel read alignment algorithm that only seeks the proposed simple and parallel in-memory operations (i.e. comparisons and additions). AlignS is then optimized through a new correlated data partitioning and mapping methodology that allows local storage and processing of DNA sequence to fully exploit the algorithm-level's parallelism, and to accelerate both exact and inexact matches. The device-to-architecture co-simulation results show that AlignS improves the short read alignment throughput per Watt per mm 2 by ~12× compared to the ASIC accelerator. Compared to recent FM-index-based ReRAM platform, AlignS achieves 1.6× higher throughput per Watt.
Author Angizi, Shaahin
Fan, Deliang
Zhang, Wei
Sun, Jiao
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  fullname: Fan, Deliang
  organization: Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL, 32816
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Snippet Classified as a complex big data analytics problem, DNA short read alignment serves as a major sequential bottleneck to massive amounts of data generated by...
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SubjectTerms Bioinformatics
Computer architecture
DNA
Genomics
Magnetic tunneling
Micromechanical devices
Sequential analysis
Title AlignS: A Processing-In-Memory Accelerator for DNA Short Read Alignment Leveraging SOT-MRAM
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