Abstract
Language | English |
---|---|
Title of host publication | 2014 27th International Conference on VLSI Design and 2014 13th International Conference on Embedded Systems |
Pages | 306-311 |
Number of pages | 6 |
DOIs | |
Publication status | Published - 1 Jan 2014 |
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Keywords
- field programmable gate arrays
- genomics
- FPGA
- Velvet
- genome assembly acceleration
- hard embedded blocks
- speedups
- Acceleration
- Assembly
- Bioinformatics
- Field programmable gate arrays
- Genomics
- Software
- Vectors
- FPGA based Acceleration
- Genome Assembly
- Hard Embedded Blocks
- NGS assembly
Cite this
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Accelerating Genome Assembly Using Hard Embedded Blocks in FPGAs. / Varma, B. S. C.; Paul, K.; Balakrishnan, M.
2014 27th International Conference on VLSI Design and 2014 13th International Conference on Embedded Systems. 2014. p. 306-311.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
TY - GEN
T1 - Accelerating Genome Assembly Using Hard Embedded Blocks in FPGAs
AU - Varma, B. S. C.
AU - Paul, K.
AU - Balakrishnan, M.
PY - 2014/1/1
Y1 - 2014/1/1
N2 - Modern FPGAs consist of a number of Hard Embedded Blocks (HEBs) like BRAMs, DSPs, PCI controllers, etc. for performing specialized operations/functions. This helps in developing efficient architectures for accelerating compute intensive kernels. Computational genomics is a fairly recent domain which helps in the understanding of the biological properties of an organism with applications in medicine, evolutionary biology and social sciences. A key problem in this research domain is the assembly of DNA sequences obtained from sequencing machines. Next Generation DNA Sequencing (NGS) technologies generate a large number of short fragments (sequences) of fixed length known as reads, which are a part of the genome sequence being assembled. It is computationally very time consuming to assemble these short reads to form the genome sequence purely with software. FPGAs have been effectively used to build accelerators to speed up the computation process. In this paper, we propose HEBs to accelerate the genome assembly process. We show 20% increase in speedups using FPGAs with HEBs over existing FPGA implementation. Speedups of up-to 11x can be obtained over Velvet [1] which is a commonly used software implementation.
AB - Modern FPGAs consist of a number of Hard Embedded Blocks (HEBs) like BRAMs, DSPs, PCI controllers, etc. for performing specialized operations/functions. This helps in developing efficient architectures for accelerating compute intensive kernels. Computational genomics is a fairly recent domain which helps in the understanding of the biological properties of an organism with applications in medicine, evolutionary biology and social sciences. A key problem in this research domain is the assembly of DNA sequences obtained from sequencing machines. Next Generation DNA Sequencing (NGS) technologies generate a large number of short fragments (sequences) of fixed length known as reads, which are a part of the genome sequence being assembled. It is computationally very time consuming to assemble these short reads to form the genome sequence purely with software. FPGAs have been effectively used to build accelerators to speed up the computation process. In this paper, we propose HEBs to accelerate the genome assembly process. We show 20% increase in speedups using FPGAs with HEBs over existing FPGA implementation. Speedups of up-to 11x can be obtained over Velvet [1] which is a commonly used software implementation.
KW - field programmable gate arrays
KW - genomics
KW - FPGA
KW - Velvet
KW - genome assembly acceleration
KW - hard embedded blocks
KW - speedups
KW - Acceleration
KW - Assembly
KW - Bioinformatics
KW - Field programmable gate arrays
KW - Genomics
KW - Software
KW - Vectors
KW - FPGA based Acceleration
KW - Genome Assembly
KW - Hard Embedded Blocks
KW - NGS assembly
U2 - 10.1109/VLSID.2014.59
DO - 10.1109/VLSID.2014.59
M3 - Conference contribution
SP - 306
EP - 311
BT - 2014 27th International Conference on VLSI Design and 2014 13th International Conference on Embedded Systems
ER -