Installation

From Bioconda

conda install -c bioconda cuttlefish

The Conda package supports k values up to 127. For larger k, install from source and see Larger k-mer sizes.

From source

git clone https://github.com/COMBINE-lab/cuttlefish.git
cd cuttlefish/
mkdir build && cd build/
cmake -DCMAKE_INSTALL_PREFIX=../ ..
make -j 8 install
cd ..

Replace 8 in make -j 8 with the number of threads you want to build with.

This installs Cuttlefish into a bin subdirectory inside the project root. To choose a different location, pass its path as -DCMAKE_INSTALL_PREFIX:

cmake -DCMAKE_INSTALL_PREFIX=<custom_path>/ ..

The executable then lands in <custom_path>/bin/. Omitting -DCMAKE_INSTALL_PREFIX entirely installs to /usr/local/bin/, which may require sudo make -j 8 install.

Note

A source installation supports k up to 63 by default — lower than the Conda package’s 127. To raise it, see Larger k-mer sizes.

Which branch

Cuttlefish 1 and 2 live on the cuttlefish-1-2 branch (their integration history is on develop-legacy):

git clone --branch cuttlefish-1-2 https://github.com/COMBINE-lab/cuttlefish.git

The initial C++ implementation of Cuttlefish 3 is preserved on the cuttlefish3-cpp branch — see The C++ Cuttlefish 3.

The repository’s default branch, main, contains only the Rust Cuttlefish 3; the C++ sources were removed from it, so a checkout of any of these branches gives you one implementation and one build system.