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

M. M.Imdad Ullah, Akram Ben Ahmed, Hideharu Amano

研究成果: Conference contribution


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.

ホスト出版物のタイトルApplied Reconfigurable Computing. Architectures, Tools, and Applications - 16th International Symposium, ARC 2020, Proceedings
編集者Fernando Rincón, Jesús Barba, Julián Caba, Hayden K.H. So, Pedro Diniz
出版ステータスPublished - 2020
イベント16th International Symposium on Applied Reconfigurable Computing, ARC 2020 - Toledo, Spain
継続期間: 2020 4 12020 4 3


名前Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
12083 LNCS


Conference16th International Symposium on Applied Reconfigurable Computing, ARC 2020

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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