A Hybrid Architecture for the Approximate String Matching on an FPGA

Next generation sequencing technologies have noticeably improved in the last decade. Time and cost of whole genome sequencing are important challenges that must be reduced, opening unprecedented opportunities to various research and development areas. The alignment or mapping of small reads produced by sequencing machines to reference genomes of billions of nucleotides is a fundamental task in this sequencing process. It is computationally highly demanding and has become the bottleneck of the DNA analysis process. This paper proposes hardware acceleration based on FPGA of the Myers bit-parallelized algorithm, appropriately modified to be used in the extend stage of DNA alignment tools. The proposed design can be employed in conjunction with software functions, as it constitutes an extremely fast heterogeneous DNA alignment system. The implementation results show a speedup of up to [Formula: see text] relative to a sequential implementation only in software. In addition, due to the limited use of FPGA resources and the modular design, multiple modules can be used to completely populate the chip, further increasing the computing speed.

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A Hybrid Architecture for the Approximate String Matching on an FPGA

Cited by 3 publications

References 12 publications

A Hardware Accelerator for Long Sequence Alignment with the Bit-Vector Scoring Scheme and Divide-and-Conquer Traceback

A Hardware Accelerator for Long Sequence Alignment with the Bit-Vector Scoring Scheme and Divide-and-Conquer Traceback

Hardware-Algorithm Codesign for Fast and Energy Efficient Approximate String Matching on FPGA for Computational Biology

Bit-Vector-Based Hardware Accelerator for DNA Alignment Tools

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