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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Vydáno v:2023 60th ACM/IEEE Design Automation Conference (DAC) s. 1 - 4
Hlavní autoři: Gamaarachchi, Hasindu, Liyanage, Kisaru, Parameswaran, Sri
Médium: Konferenční příspěvek
Jazyk:angličtina
Vydáno: IEEE 09.07.2023
Témata:
Computer architecture
Genomics
Hardware
Scalability
Sequences
Sequential analysis
Software algorithms
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Shrnutí: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