tkoohi / spruce

SPRUCE: Somatic Phylogeny Reconstruction using Combinatorial Enumeration

SPRUCE

SPRUCE (Somatic Phylogeny Reconstruction using Combinatorial Enumeration) is an algorithm for inferring the clonal evolution of single-nucleotide and copy-number variants given multi-sample bulk tumor sequencing data.

License

Support

For support using SPRUCE, please visit the SPRUCE Google Group.

Dependencies

SPRUCE is written C++. In addition to a recent C++ compiler (that supports C++11), it has the following dependencies:

• CMake (>= 2.8)
• Boost (>= 1.38)
• LEMON graph library (>= 1.3)

Graphviz is required to visualize the resulting DOT files, but is not required for compilation.

Compilation instructions

To compile SPRUCE, execute the following commands from the root of the repository:

mkdir build
cd build
cmake ..
make

In case CMake fails to detect LEMON, run the following command with adjusted paths:

cmake -DLIBLEMON_ROOT=~/lemon ..

The compilation results in the following files in the build directory:

EXECUTABLE	DESCRIPTION
cliques	Enumerates cliques of the compatibility graph (given a size and a filter)
enumerate	Enumerates perfect phylogeny trees
merge	Merges multiple solution files into one
rank	Sorts solution trees by the fraction of common edges (solution with rank 0 is the most representative tree)
visualize	Visualizes one solution or the entire solution space

For example usage see result/run_A22.sh and corresponding instructions. For a description of the input file format see data/README.md.

For instructions on how to visualize the set of enumerated trees see src/visualization/README.md.