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Title: GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping
Authors: Alser, Mohammed
Hassan, Hasan
Xin, Hongyi
Ergin, Oğuz
Mutlu, Onur
Alkan, Can
Keywords: Genome
read mapping
Issue Date: 1-Nov-2017
Publisher: Oxford Univ Press
Source: Alser, M., Hassan, H., Xin, H., Ergin, O., Mutlu, O., & Alkan, C. (2017). GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. Bioinformatics, 33(21), 3355-3363.
Abstract: Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments - called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and 'candidate' locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper's execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms. Results: We propose GateKeeper, a new hardware accelerator that functions as a pre-alignment step that quickly filters out most incorrect candidate locations. GateKeeper is the first design to accelerate pre-alignment using Field-Programmable Gate Arrays (FPGAs), which can perform pre-alignment much faster than software. When implemented on a single FPGA chip, GateKeeper maintains high accuracy (on average >96%) while providing, on average, 90-fold and 130-fold speedup over the state-of-the-art software pre-alignment techniques, Adjacency Filter and Shifted Hamming Distance (SHD), respectively. The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10.
ISSN: 1367-4803
Appears in Collections:Bilgisayar Mühendisliği Bölümü / Department of Computer Engineering
PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

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