BarraCUDA Fast Short Read Aligner Icon

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


  • Fixed problems with compiling the software in Ubuntu 16.04
  • Tweak: SAMPE 8-core limit is now lifted
  • 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


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Additional Project Details

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Programming Language

C++, C



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