klue is a C++ program for pseudoassembly with k-mers. The program uses the Bifrost colored de Bruijn graph for indexing. For details on the method and its applications, see the preprint describing the klue program: Pseudoassembly of k-mers by Delaney K Sullivan, Mayuko Boffelli, and Lior Pachter.
To build klue, you need the following:
- A C++17-compatible compiler (e.g., AppleClang 15+, GCC 7+, or newer)
- Bifrost installed with:
- Headers in
/usr/local/include/bifrost - Library in
/usr/local/lib/libbifrost.aor.dylib
- Headers in
- Zlib (preinstalled on macOS and most Linux distributions)
Clone the repository and build using CMake:
git clone https://github.com/pachterlab/klue.git
cd klue
mkdir build
cd build
cmake ..
make -j
sudo make installAfter installation, run klue from the command line:
klue 0.29.0
Usage: klue <CMD> [arguments] ..
Where <CMD> can be one of:
distinguish Extracts distinguishing contigs from FASTA/FASTQ files
refine Refine contigs based on certain criteria
version Prints version information
cite Prints citation information