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Bioinformatics. 2017 Nov 1;33(21):3355-3363. doi: 10.1093/bioinformatics/btx342.

GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.

Author information

1
Department of Computer Engineering, Bilkent University, Bilkent, Ankara 06800, Turkey.
2
TOBB University of Economics & Technology, Sogutozu, Ankara, Turkey.
3
Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland.
4
Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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.

Availability and implementation:

https://github.com/BilkentCompGen/GateKeeper.

Contact:

mohammedalser@bilkent.edu.tr or onur.mutlu@inf.ethz.ch or calkan@cs.bilkent.edu.tr.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28575161
PMCID:
PMC5860160
[Available on 2018-11-01]
DOI:
10.1093/bioinformatics/btx342
[Indexed for MEDLINE]

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