Accelerating Genome Analysis: A Primer on an Ongoing Journey

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 t...

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Bibliographic Details
Published in:IEEE MICRO 2020-09, Vol.40 (5), p.65-75
Main Authors: Alser, Mohammed, Bingol, Zulal, Cali, Damla Senol, Kim, Jeremie, Ghose, Saugata, Alkan, Can, Mutlu, Onur
Format: Article
Language:English
Subjects:
Algorithms
Bioinformatics
Computer architecture
Gene sequencing
Genomes
Genomics
Hardware
Indexing
Mapping
Memory management
Sequential analysis
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Summary: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.
ISSN:0272-1732
1937-4143
DOI:10.1109/MM.2020.3013728