FAssem: FPGA Based Acceleration of De Novo Genome Assembly

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

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

20 Citations (Scopus)


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 languageEnglish
Title of host publication2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines
PublisherIEEE Xplore
Number of pages4
ISBN (Electronic)9780769549699
ISBN (Print)9781467360050
Publication statusPublished (in print/issue) - 25 Jun 2013


  • 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


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