FAssem: FPGA Based Acceleration of De Novo Genome Assembly

Sharatchandra Varma Bogaraju, Kolin Paul, M Balakrishnan, D. Lavenier

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

18 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.
Original languageUndefined/Unknown
Title of host publication2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines
Pages173-176
Number of pages4
DOIs
Publication statusPublished - 01 Apr 2013
Externally publishedYes

Keywords

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

Cite this

Bogaraju, S. V., Paul, K., Balakrishnan, M., & Lavenier, D. (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