Hardware acceleration of de novo genome assembly

B. Sharat Chandra Varma, Kolin Paul, Balakrishnan. M, Dominique Lavenier

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Abstract

The cost of genome assembly has gone down drastically with the advent of next generation sequencing technologies. These new sequencing technologies produce large amounts of DNA fragments. Software programs are used to construct the genome from these DNA fragments. The assembly programs take significant amount of time to execute. To reduce the execution time, these programs are being parallelised to take advantage of many cores available in present day processor chips. Further, hardware accelerators have been developed which when used along with processors speed up the execution. Velvet is a commonly used software for de novo assembly. We propose a novel method to reduce the overall time of assembly by using FPGAs. In this method, we perform pre-processing of these short reads on FPGAs and process the output using Velvet to reduce the overall time for assembly. We show that using our technique we can get significant speed-ups.
Original languageEnglish
Pages (from-to)74-89
Number of pages16
JournalInternational Journal of Embedded Systems
Volume9
Issue number1
Early online date21 Jan 2017
DOIs
Publication statusE-pub ahead of print - 21 Jan 2017

Keywords

  • Hardware Implementation
  • Bioinformatics
  • Hardware Acceleration
  • Genome Assembly
  • Field Programmable Gate Array (FPGA)

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    Varma, B. S. C., Paul, K., M, B., & Lavenier, D. (2017). Hardware acceleration of de novo genome assembly. International Journal of Embedded Systems, 9(1), 74-89. https://doi.org/10.1504/IJES.2017.081729