Implementation of FM-Index Based Pattern Search on a Multi-FPGA System

  • M. M. Imdad UllahEmail author
  • Akram Ben Ahmed
  • Hideharu Amano
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 12083)


Pattern matching is a versatile task which has a variety of applications including genome sequencing as a major application. During the analysis, short read mapping technique is used where short DNA sequences are mapped relative to a known reference sequence. This paper discusses the use of reconfigurable hardware to accelerate the short read mapping problem. The proposed design is based on the FM-index algorithm. Although several pattern matching techniques are available, FM-index based pattern search is perfectly suitable for genome sequencing due to the fastest mapping from known indices. In order to make use of inherent parallelism, a multi-FPGA system called Flow-in-Cloud (FiC) is used. FiC consists of multiple boards, mounting middle scale Xilinx’s FPGAs and SDRAMs, which are tightly coupled with high speed serial links. By distributing the input data transfer with I/O ring network and broadcasting I-Table, C-Table and Suffix-Array with the board-to-board interconnection network, about 10 times performance improvement was achieved when compared to the software implementation. Since the proposed method is scalable to the number of boards, we can obtain the required performance by increasing the number of boards.


  1. 1.
    Arram, J., Kaplan, T., Luk, W., Jiang, P.: Leveraging FPGAs for accelerating short read alignment. IEEE/ACM Trans. Comput. Biol. Bioinform. 14, 668–677 (2017)CrossRefGoogle Scholar
  2. 2.
    Arram, J., Tsoi, K.H., Luk, W., Jiang, P.: Hardware acceleration of genetic sequence alignment. In: Brisk, P., de Figueiredo Coutinho, J.G., Diniz, P.C. (eds.) ARC 2013. LNCS, vol. 7806, pp. 13–24. Springer, Heidelberg (2013). Scholar
  3. 3.
    Burrows, M., Wheeler, D.J.: A block-sorting lossless data compression algorithm. Technical report (1994)Google Scholar
  4. 4.
    Fernandez, E., Najjar, W., Lonardi, S.: String matching in hardware using the FM-index. In: 2011 IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines, pp. 218–225, May 2011Google Scholar
  5. 5.
    Ferragina, P., Manzini, G.: Opportunistic data structures with applications. In: Proceedings 41st Annual Symposium on Foundations of Computer Science, pp. 390–398, November 2000Google Scholar
  6. 6.
    Hironaka, K., Doan, N.A.V., Amano, H.: Towards an optimized multi FPGA architecture with STDM network: a preliminary study. In: Voros, N., Huebner, M., Keramidas, G., Goehringer, D., Antonopoulos, C., Diniz, P.C. (eds.) ARC 2018. LNCS, vol. 10824, pp. 142–150. Springer, Cham (2018). Scholar
  7. 7.
    Langmead, B., Trapnell, C., Pop, M., Salzberg, S.L.: Ultrafast and memory-efficient alignment of short dna sequences to the human genome. Genome Biol. 10(3), R25 (2009)CrossRefGoogle Scholar
  8. 8.
    Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14), 1754–1760 (2009)CrossRefGoogle Scholar
  9. 9.
    Liu, C.-M., et al.: SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics 28(6), 878–879 (2012)CrossRefGoogle Scholar
  10. 10.
    Olson, C., et al.: Hardware acceleration of short read mapping. In: IEEE 20th International Symposium on Field-Programmable Custom Computing Machines (FCCM), pp. 161–168 (2012)Google Scholar
  11. 11.
    Samtec, Inc.: Micro Flyover On-Board Optical Engine, FireFly.
  12. 12.
    Yamakura, M., Hironaka, K., Azegami, K., Musha, K., Amano, H.: The evaluation of partial reconfiguration for a multi-board FPGA system FiCsw. In: Proceedings of the 10th International Symposium on Highly-Efficient Accelerators and Reconfigurable Technologies, HEART 2019, pp. 15:1–15:4 (2019)Google Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • M. M. Imdad Ullah
    • 1
    Email author
  • Akram Ben Ahmed
    • 1
  • Hideharu Amano
    • 1
  1. 1.Department of Information and Computer ScienceKeio UniversityYokohamaJapan

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