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).