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BarraCUDA Fast Short Read Aligner

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Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.

BarraCUDA Fast Short Read Aligner Web Site


  • IMPORTANT FIX: please download 0.7.105a which fixes the memory leak in SAMPE command
  • NEW RELEASE ver 0.7 - compatible with BWA 0.6+ BWT index
  • Many thanks to Drs Bill Langdon and Arran Schlosberg for their contributions to the new code.
  • Much faster than ver. 0.6.2! In fact it is now twice as fast compared to a 12 core Xeon server
  • FM-index sequencing read mapper software using NVIDIA CUDA acceleration
  • Outputs in SAM format for downstream analyses
  • Requires NVIDIA graphics card with compute capability 3.5 or above and at least 1GB VRAM
  • Requires NVIDIA CUDA SDK toolkit 6.x or above and NVIDIA driver 340 or above
  • BarraCUDA is published on BMC Research Notes 2012, 5:27, doi:10.1186/1756-0500-5-27
  • Paper URL:
  • This project is supported by the CUDA centre of excellence at Cambridge University


Additional Project Details

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User Interface


Programming Language

C++, C


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