Single pass streaming BLAST on FPGAs

Herbordt, Martin C.; Model, J.; Sukhwani, Bharat; Gu, Yongfeng; VanCourt, T.

doi:10.1016/j.parco.2007.09.003

Cited by 36 publications

(10 citation statements)

References 19 publications

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“…There are FPGA and GPU implementations of the SmithWaterman algorithm [9]- [11] and accelerators for BLAST [21]- [23] available. These mappers boost performance using large numbers of parallel computation units.…”

Section: Mappers On Parallel Platformsmentioning

confidence: 99%

PoC-align: An open-source alignment accelerator using FPGAs

Preuser

Knodel

Spallek

2014

2014 International Conference on ReConFigurable Computing and FPGAs (ReConFig14)

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The mapping of reads, i.e. short DNA base pair strings, to large genome databases has become a critical operation for genetic analysis and diagnosis. The underlying alignment operation essentially is a string search tolerating some character mismatches and possibly character deletions or insertions with respect to a reference genome. Its output comprises the locations within the reference that are likely to correspond to the mapped DNA snippet.This paper describes PoC-Align, an alignment infrastructure using FPGA accelerators. It is an extension of our preceding FPGA aligner [1], which has been enhanced to tolerate alignment gaps (insertions and deletions) and to be more customizable though generic parameters. In addition to the descriptions of the implementation of these extensions, we also name the mainly software-carried enhancements, such as the support of mapping paired-end reads, that are implemented on top of the FPGA accelerator. Providing a thorough overview on the complete infrastructure, we aim at advertising the disclosure of the sources of our solution and hope to encourage other groups to use and extend this platform.

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Section: Mappers On Parallel Platformsmentioning

confidence: 99%

PoC-align: An open-source alignment accelerator using FPGAs

Preuser

Knodel

Spallek

2014

2014 International Conference on ReConFigurable Computing and FPGAs (ReConFig14)

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“…The exhaustive ungapped alignment (EUA) filter is based on the TreeBLAST scheme described in [8]. The EUA filter has two essential properties.…”

Section: Accelerated Blastp Overviewmentioning

confidence: 99%

“…BLAST acceleration has therefore received much attention with FPGAs being successfully applied. There have been commercial products from TimeLogic [19], Mitrionics [15], and Convey [6] and several academic efforts [8,10,11,16,17,18,22]. GPU implementations described in published studies [12,21,20] have so far achieved performance up to about 2.5x times that of a multicore CPU running a version of NCBI BLAST that has now been superceded by a faster version.…”

Section: Introductionmentioning

confidence: 99%

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NCBI BLASTP on the convey HC1-EX

Mahram

Herbordt

2013

SIGARCH Comput. Archit. News

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The BLAST sequence alignment program is a central application in bioinformatics. The de facto standard version, NCBI BLAST, uses complex heuristics which make it challenging to simultaneously achieve both high performance and exact agreement. In previous work, a system that used novel FPGA-based filters reduced the input database by over 99.97% without loss of sensitivity. In the present work we report experiences in getting from a prototype to a potential product for the Convey HC1-EX. There are several issues. The first is the efforts made to maintain timing for a highly complex configuration as it is optimized by including additional filter stages. This requires implementation and optimization of new interface logic as well as floor-planning. The second is the system-level tradeoffs necessary to maintain correctness. The issue here is preventing low frequency events, which necessarily cannot be mapped to the FPGA, from diluting the performance benefits without sacrificing sensitivity. We present results for various usage scenarios and find a factor of nearly 5x speed-up over a fully parallel implementation of the reference code on a contemporaneous CPU. We believe that the resulting system is the leading accelerated NCBI BLAST. The significance of this work is that, while such in-depth work is necessary to achieve highperformance for complex systems, these issues are rarely described in the academic literature.

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“…This application has seen a number of accelerated implementations, including TreeBLAST [10], RC-BLAST [7], and Mercury BLAST [5], among others. All of the above implementations use FPGAs as co-processors.…”

Section: Introductionmentioning

confidence: 99%

Bloom Filter Performance on Graphics Engines

Chamberlain

Buhler

et al. 2011

2011 International Conference on Parallel Processing

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Abstract-Bloom filters are a probabilistic technique for large-scale set membership tests. They exhibit no false negative test results but are susceptible to false positive results. They are well-suited to both large sets and large numbers of membership tests. We implement the Bloom filters present in an accelerated version of BLAST, a genome biosequence alignment application, on NVIDIA GPUs and develop an analytic performance model that helps potential users of Bloom filters to quantify the inherent tradeoffs between throughput and false positive rates.

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Single pass streaming BLAST on FPGAs

Cited by 36 publications

References 19 publications

PoC-align: An open-source alignment accelerator using FPGAs

PoC-align: An open-source alignment accelerator using FPGAs

NCBI BLASTP on the convey HC1-EX

Bloom Filter Performance on Graphics Engines

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