Hardware-Acceleration of Short-Read Alignment Based on the Burrows-Wheeler Transform

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13 Citations (Scopus)


The alignment of millions of short DNA fragments to a large genome is a very important aspect of the modern computational biology. However, software-based DNA sequence alignment takes many hours to complete. This paper proposes an FPGA-based hardware accelerator to reduce the alignment time. We apply a data encoding scheme that reduces the data size by 96 percent, and propose a pipelined hardware decoder to decode the data. We also design customized data paths to efficiently use the limited bandwidth of the DDR3 memories. The proposed accelerator can align a few hundred million short DNA fragments in an hour by using 80 processing elements in parallel. The proposed accelerator has the same mapping quality compared to the software-based methods.

Original languageEnglish
Article number7122348
Pages (from-to)1358-1372
Number of pages15
JournalIEEE Transactions on Parallel and Distributed Systems
Issue number5
Publication statusPublished - 2016 May 1


  • Burrows-Wheeler alignment
  • FPGA accelerator
  • genome mapping
  • Short-read alignment


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