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

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

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
Volume27
Issue number5
DOIs
Publication statusPublished - 2016 May 1

Keywords

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

ASJC Scopus subject areas

  • Signal Processing
  • Hardware and Architecture
  • Computational Theory and Mathematics

Fingerprint Dive into the research topics of 'Hardware-Acceleration of Short-Read Alignment Based on the Burrows-Wheeler Transform'. Together they form a unique fingerprint.

  • Cite this