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genome sequence alignment
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README.md

AnySeq

Proof-of-concept sequence alignment algorithms library implemented in Impala.

Setup Instructions

  • Prerequisites:

  • a recent version of CMake (at least v3.7)

  • for the CUDA benchmark an NVIDIA GPU with recent drivers and a working CUDA installation

  • make sure, that the CUDA libraries are in your PATH before installing AnyDSL

  • Install AnyDSL. In order to do so, run the "install_anydsl.sh" script provided. This will download, configure & compile AnyDSL which can take some time.

  • After you have a working AnyDSL installation you can run the AnySeq build script:

./makeall.sh <absolute path to your AnyDSL installation>

If all went well you should now have two different executables for CPU and GPU.

Running

Demo Benchmarks

The 'bechmark.sh' script will align two bacterial genomes and 2 random sequences with different alignment schemes for the CPU and the GPU version.

Demo Program Usage

  • read sequences from files:

    align [-o <output_file>] -i <FASTA file> <FASTA file>
    
  • use random sequences:

    align [-o <output_file>] -r [[<min length>] <max length>]
    
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