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