Accelerating Genome Analysis: A Primer on an Ongoing Journey
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Date
2020
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Journal Article
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yes
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Abstract
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis pipeline, because state-of-the-art genome sequencing technologies are able to sequence a genome much faster than the computational techniques employed to analyze the genome. We describe the ongoing journey in significantly improving the performance of read mapping. We explain state-of-the-art algorithmic methods and hardware-based acceleration approaches. Algorithmic approaches exploit the structure of the genome as well as the structure of the underlying hardware. Hardware-based acceleration approaches exploit specialized microarchitectures or various execution paradigms (e.g., processing inside or near memory). We conclude with the challenges of adopting these hardware-accelerated read mappers. © 2020 IEEE.
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published
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40 (5)
Pages / Article No.
65 - 75
Publisher
IEEE
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Software
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09483 - Mutlu, Onur / Mutlu, Onur