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BarraCUDA

Allows users to align large numbers of next generation DNA sequences. BarraCUDA uses the Burrows-Wheeler algorithm. This software aligns short noisy DNA sequences against one of the increasing number of reference genomes. It can align human DNA sequences when run on nVidia consumer Graphics processing unit (GPU) cards with more than 4 GB of memory, e.g. the GeForce GT 730. The software was built with default setting and a second version was built specifically for the GT 730.

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BarraCUDA classification

BarraCUDA specifications

Software type:
Application/Script, Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
Parallelization:
CUDA
Version:
0.7.107
Requirements:
NVIDIA CUDA toolkit SDK, GCC, G++, NVIDIA graphics driver, zlib-devel (or zlib1g-dev) library
Interface:
Command line interface
Output format:
SAM
Programming languages:
C
Computer skills:
Advanced
Stability:
Beta
Maintained:
Yes

BarraCUDA distribution

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BarraCUDA support

Maintainers

  • WIlliam Langdon <>
  • Brian Lam <>

Credits

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Publications

Institution(s)

Department of Computer Science, University College London, Gower Street, London, UK; University of Cambridge Metabolic Research Laboratories, Addenbrooke’s Hospital, Cambridge, UK

Funding source(s)

Supported by the EPSRC (grant EP/M025853/1).

Link to literature

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