Implementation of a custom hardware-accelerator for short-read mapping using Burrows-Wheeler alignment

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

6 Citations (Scopus)

Abstract

The mapping of millions of short DNA fragments to a large genome is a great challenge in modern computational biology. Usually, it takes many hours or days to map a large genome using software. However, the recent progress of programmable hardware such as field programmable gate arrays (FPGAs) provides a cost effective solution to this challenge. FPGAs contain millions of programmable logic gates to design massively parallel accelerators. This paper proposes a hardware architecture to accelerate the short-read mapping using Burrows-Wheeler alignment. The speed-up of the proposed architecture is estimated to be at least 10 times compared to its equivalent software application.

Original languageEnglish
Title of host publication2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013
Pages651-654
Number of pages4
DOIs
Publication statusPublished - 2013
Event2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013 - Osaka, Japan
Duration: 2013 Jul 32013 Jul 7

Publication series

NameProceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
ISSN (Print)1557-170X

Other

Other2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013
Country/TerritoryJapan
CityOsaka
Period13/7/313/7/7

Keywords

  • FPGA
  • sequence alignment
  • short-read mapping

ASJC Scopus subject areas

  • Signal Processing
  • Biomedical Engineering
  • Computer Vision and Pattern Recognition
  • Health Informatics

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