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      • Department of Computer Engineering
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      Accelerating genome analysis: a primer on an ongoing journey

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      Author(s)
      Alser, M.
      Zülal, Bingöl
      Cali, D. S.
      Kim, J.
      Ghose, S.
      Alkan, Can
      Mutlu, Onur
      Date
      2020
      Source Title
      IEEE Micro
      Print ISSN
      0272-1732
      Publisher
      IEEE
      Volume
      40
      Issue
      5
      Pages
      65 - 75
      Language
      English
      Type
      Article
      Item Usage Stats
      73
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      41
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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.
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      http://hdl.handle.net/11693/55077
      Published Version (Please cite this version)
      https://dx.doi.org/10.1109/MM.2020.3013728
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