Parallel Implementation for Partitioning HTS Read Datasets and Associated de Bruijn Graph

Code organization

Note

• The current version corresponds to an alpha release of the software
• Additional usage instructions are to follow
• External (third-party) softwares, included in the ext/ directory, are covered under their repective licenses

Dependencies

• cmake version >= 2.6
• g++ (version 4.8.1+)
• an MPI implementation supporting MPI-2 or MPI-3
• external (third-party) softwares are included in the ext/ directory of this project

Download and compile

The repository and external submodules can be downloaded using the recursive clone.

git clone --recursive <URL>

Set up external submodule (ext/bliss/ext/sparsehash).

./configure
make

Compile using the cmake tool.

mkdir build_directory && cd build_directory
cmake ../read_partitioning
make -j <THREAD COUNT>

Run

Inside the build directory,

mpirun -np <COUNT OF PROCESSES> ./bin/<EXECUTABLE> <ARGUMENTS>