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CRiSPy

Computing Species Richness in 16S rRNA Pyrosequencing Datasets

Run

  • To run CRiSPy
./crispy.sh <input_fasta_file> [k_value] [band_value]
  • k_value: parameter for kmer distance computation. By default: 6
  • band_value: parameter of banded global alignment for genetic distance computation. By default: 10 i.e. 1/10 banded alignment

Require

  • Hardware:
    • NVIDIA GPU card of compute capability 2.0 or above
  • Software:
    • Linux operating system, preferably Ubuntu
    • CUDA toolkit installed for code compilation
    • GCC installed for code compilation
    • R with R changepoint package installed for code execution

Compile

  • To compile:
./compile.sh
  • To compile with for an NVIDIA GPU with compute capability other than 5.0. For example for a Fermi card with compute capability 2.0:
./compile.sh 20

License

The project is licensed under the GPL 3.0 license (http://www.gnu.org/licenses/gpl.html).