Hardware Acceleration of Smith-Waterman Algorithm for Short Read DNA Alignment Using FPGA

2016 ◽  
Author(s):  
Wael Abou El-Wafa ◽  
Asmaa G. Seliem ◽  
Hesham F. A. Hamed
Keyword(s):  
Hardware Acceleration ◽  
Short Read ◽  
Dna Alignment

Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths

2018 ◽  
Vol 75 ◽  
pp. 54-64 ◽  
Author(s):  
Ernst Joachim Houtgast ◽  
Vlad-Mihai Sima ◽  
Koen Bertels ◽  
Zaid Al-Ars
Keyword(s):  
Hardware Acceleration ◽  
Read Mapping ◽  
Short Read ◽  
Short Read Mapping

Bit-Vector-Based Hardware Accelerator for DNA Alignment Tools

2020 ◽  
pp. 2150087
Author(s):  
Daniel Pacheco Bautista ◽  
Ricardo Carreño Aguilera ◽  
Francisco Aguilar Acevedo ◽  
Ignacio Algredo Badillo
Keyword(s):  
Dna Analysis ◽  
Modular Design ◽  
Hardware Acceleration ◽  
Sequencing Technologies ◽  
Analysis Process ◽  
Alignment System ◽  
Bit Vector ◽  
Dna Alignment ◽  
Reference Genomes ◽  
Generation Sequencing

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.

From sequencing to hardware acceleration of DNA alignment software: A integral review

2015 ◽  
Vol 36 (3) ◽  
pp. 257-275 ◽  
Author(s):  
D Pacheco Bautista ◽  
M González Pérez ◽  
I Algredo Badillo
Keyword(s):  
Hardware Acceleration ◽  
Dna Alignment

Hardware Acceleration of Short Read Mapping

2012 ◽  
Author(s):  
Corey B. Olson ◽  
Maria Kim ◽  
Cooper Clauson ◽  
Boris Kogon ◽  
Carl Ebeling ◽  
...  
Keyword(s):  
Hardware Acceleration ◽  
Read Mapping ◽  
Short Read ◽  
Short Read Mapping

Hardware Acceleration of Bilateral Filters

2013 ◽  
Vol 133 (2) ◽  
pp. 132-138
Author(s):  
Shuhei Isa ◽  
Chikatoshi Yamada ◽  
Yasunori Nagata
Keyword(s):  
Hardware Acceleration ◽  
Bilateral Filters

The real-time computing of the Stirling formula based on hardware acceleration

2013 ◽  
Author(s):  
Jiyang Yu ◽  
Dan Huang ◽  
Siyang Zhao ◽  
Nan Pei ◽  
Huixia Cheng ◽  
...  
Keyword(s):  
Real Time ◽  
Hardware Acceleration ◽  
Stirling Formula ◽  
The Real ◽  
Real Time Computing
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