Hyper customized processors for bio-sequence database scanning on FPGAs

Oliver, Tim; Schmidt, Bertil; Maskell, Douglas L.

doi:10.1145/1046192.1046222

Cited by 86 publications

(76 citation statements)

References 13 publications

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“…For example, a 150-PE array could present itself as two separate 75-PE arrays. This is similar to the approach suggested in [11]. However, that technique needs substantial additional hardware resources.…”

Section: Definitionmentioning

confidence: 59%

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An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm

Houtgast

Sima

Bertels

et al. 2015

2015 International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation (SAMOS)

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Abstract-We present the first accelerated implementation of BWA-MEM, a popular genome sequence alignment algorithm widely used in next generation sequencing genomics pipelines. The Smith-Waterman-like sequence alignment kernel requires a significant portion of overall execution time. We propose and evaluate a number of FPGA-based systolic array architectures, presenting optimizations generally applicable to variable length Smith-Waterman execution. Our kernel implementation is up to 3x faster, compared to software-only execution. This translates into an overall application speedup of up to 45%, which is 96% of the theoretically maximum achievable speedup when accelerating only this kernel.

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Section: Definitionmentioning

confidence: 59%

“…Many implementations that map the Smith-Waterman algorithm onto a systolic array have been proposed, amongst others [11], [13] and [14]. A systolic array consists of Processing Elements, or PEs for short, that operate in parallel.…”

Section: ) Linear Systolic Arraysmentioning

confidence: 99%

An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm

Houtgast

Sima

Bertels

et al. 2015

2015 International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation (SAMOS)

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“…The authors of [17] built highly customizable PEs for the alignment of biological sequences on FPGA. They could implement an array of PEs of size 13 on a Spartan 3 1500 chip.…”

Section: Resultsmentioning

confidence: 99%

Optimized and Portable FPGA-Based Systolic Cell Architecture for Smith-Waterman-Based DNA Sequence Alignment

Shah¹,

Hasan²,

Koo

2016

Journal of information and communication convergence engineerin

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“…Basically, most of the research efforts such as [21]- [27] utilize systolic array or fine-grain PE architecture to accelerate PSA with affine gap penalty. Experiments show that, when compared to state-of-the-art software implementations, the reconfigurable accelerators can achieve a speedup from around 40× to 246×.…”

Section: A Pairwise Sequence Alignmentmentioning

confidence: 99%

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

Liu

Luk

2017

2017 27th International Conference on Field Programmable Logic and Applications (FPL)

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Abstract-Genetic sequence alignment has always been a computational challenge in bioinformatics. Depending on the problem size, software-based aligners can take multiple CPUdays to process the sequence data, creating a bottleneck point in bioinformatic analysis flow. Reconfigurable accelerator can achieve high performance for such computation by providing massive parallelism, but at the expense of programming flexibility and thus has not been commensurately used by practitioners. Therefore, this paper aims to provide a thorough survey of the proposed accelerators by giving a qualitative categorization based on their algorithms and speedup. A comprehensive comparison between work is also presented so as to guide selection for biologist, and to provide insight on future research direction for FPGA scientists.

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Hyper customized processors for bio-sequence database scanning on FPGAs

Cited by 86 publications

References 13 publications

An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm

An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm

Optimized and Portable FPGA-Based Systolic Cell Architecture for Smith-Waterman-Based DNA Sequence Alignment

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

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