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

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

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

4 Citations (Scopus)


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.

Original languageEnglish
Title of host publicationApplied Reconfigurable Computing. Architectures, Tools, and Applications - 16th International Symposium, ARC 2020, Proceedings
EditorsFernando Rincón, Jesús Barba, Julián Caba, Hayden K.H. So, Pedro Diniz
Number of pages16
ISBN (Print)9783030445331
Publication statusPublished - 2020
Event16th International Symposium on Applied Reconfigurable Computing, ARC 2020 - Toledo, Spain
Duration: 2020 Apr 12020 Apr 3

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume12083 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference16th International Symposium on Applied Reconfigurable Computing, ARC 2020

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)


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