Invited: Algorithms and Architectures for Accelerating Long Read Sequence Analysis

Genome sequencing is continuing to revolutionize the medical, forensics, agricultural, and biosecurity fields. The enormous amounts of data from modern sequencing technology, require significant time and cost to obtain accurate results using general-purpose computing resources. The emergence of thir...

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Bibliographic Details
Published in:2023 60th ACM/IEEE Design Automation Conference (DAC) pp. 1 - 4
Main Authors: Gamaarachchi, Hasindu, Liyanage, Kisaru, Parameswaran, Sri
Format: Conference Proceeding
Language:English
Published: IEEE 09.07.2023
Subjects:
Computer architecture
Genomics
Hardware
Scalability
Sequences
Sequential analysis
Software algorithms
Online Access:Get full text
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Summary:Genome sequencing is continuing to revolutionize the medical, forensics, agricultural, and biosecurity fields. The enormous amounts of data from modern sequencing technology, require significant time and cost to obtain accurate results using general-purpose computing resources. The emergence of third-generation sequencers called nanopore sequencers offers small, cheap, and portable genome sequencing capabilities. However, the bottleneck during computational analysis limits scalability and portability. This paper introduces the necessity for one, optimization of existing algorithms; two, efficient utilization of existing heterogeneous systems; and three, novel algorithms and domain-specific architectures for rapid in situ analysis of third-generation sequencing data. State-of-the-art examples are described and future challenges are outlined.
DOI:10.1109/DAC56929.2023.10247772