FAssem: FPGA Based Acceleration of De Novo Genome Assembly

B. S. C. Varma, K. Paul, M. Balakrishnan, D. Lavenier, Sharat Chandra Varma B

Research output: Chapter in Book/Report/Conference proceedingConference contribution

16 Citations (Scopus)

Abstract

Next generation sequencing technologies produce large amounts of data at very low cost. They produce short reads of DNA fragments. These fragments have many overlaps, lots of repeats and may also include sequencing errors. The assembly process involves merging these sequences to form the original sequences. In recent years many software programs have been developed for this purpose. All of them take significant amount of time to execute. Velvet is a commonly used de novo assembly program. We propose a method to reduce the overall time for assembly by using pre-processing of the short read data on FPGAs and processing its output using Velvet. We show significant speed-ups with slight or no compromise on the quality of the assembled output.
LanguageUndefined
Title of host publication2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines
Pages173-176
Number of pages4
DOIs
Publication statusPublished - 1 Apr 2013

Keywords

  • bioinformatics
  • DNA
  • field programmable gate arrays
  • FAssem
  • FPGA-based acceleration
  • De Novo genome assembly
  • next generation sequencing technologies
  • DNA fragments
  • sequencing errors
  • software programs
  • Velvet
  • short read data preprocessing
  • assembled output quality
  • Field programmable gate arrays
  • Assembly
  • Bioinformatics
  • Software
  • Genomics
  • Acceleration
  • Redundancy
  • FPGA
  • Next Generation Sequencing Assembly

Cite this

Varma, B. S. C., Paul, K., Balakrishnan, M., Lavenier, D., & B, S. C. V. (2013). FAssem: FPGA Based Acceleration of De Novo Genome Assembly. In 2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines (pp. 173-176) https://doi.org/10.1109/FCCM.2013.25
Varma, B. S. C. ; Paul, K. ; Balakrishnan, M. ; Lavenier, D. ; B, Sharat Chandra Varma. / FAssem: FPGA Based Acceleration of De Novo Genome Assembly. 2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines. 2013. pp. 173-176
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abstract = "Next generation sequencing technologies produce large amounts of data at very low cost. They produce short reads of DNA fragments. These fragments have many overlaps, lots of repeats and may also include sequencing errors. The assembly process involves merging these sequences to form the original sequences. In recent years many software programs have been developed for this purpose. All of them take significant amount of time to execute. Velvet is a commonly used de novo assembly program. We propose a method to reduce the overall time for assembly by using pre-processing of the short read data on FPGAs and processing its output using Velvet. We show significant speed-ups with slight or no compromise on the quality of the assembled output.",
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Varma, BSC, Paul, K, Balakrishnan, M, Lavenier, D & B, SCV 2013, FAssem: FPGA Based Acceleration of De Novo Genome Assembly. in 2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines. pp. 173-176. https://doi.org/10.1109/FCCM.2013.25

FAssem: FPGA Based Acceleration of De Novo Genome Assembly. / Varma, B. S. C.; Paul, K.; Balakrishnan, M.; Lavenier, D.; B, Sharat Chandra Varma.

2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines. 2013. p. 173-176.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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AU - B, Sharat Chandra Varma

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N2 - Next generation sequencing technologies produce large amounts of data at very low cost. They produce short reads of DNA fragments. These fragments have many overlaps, lots of repeats and may also include sequencing errors. The assembly process involves merging these sequences to form the original sequences. In recent years many software programs have been developed for this purpose. All of them take significant amount of time to execute. Velvet is a commonly used de novo assembly program. We propose a method to reduce the overall time for assembly by using pre-processing of the short read data on FPGAs and processing its output using Velvet. We show significant speed-ups with slight or no compromise on the quality of the assembled output.

AB - Next generation sequencing technologies produce large amounts of data at very low cost. They produce short reads of DNA fragments. These fragments have many overlaps, lots of repeats and may also include sequencing errors. The assembly process involves merging these sequences to form the original sequences. In recent years many software programs have been developed for this purpose. All of them take significant amount of time to execute. Velvet is a commonly used de novo assembly program. We propose a method to reduce the overall time for assembly by using pre-processing of the short read data on FPGAs and processing its output using Velvet. We show significant speed-ups with slight or no compromise on the quality of the assembled output.

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Varma BSC, Paul K, Balakrishnan M, Lavenier D, B SCV. FAssem: FPGA Based Acceleration of De Novo Genome Assembly. In 2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines. 2013. p. 173-176 https://doi.org/10.1109/FCCM.2013.25