Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit.
- Use the precompiled binaries (Linux X86) or Docker image from the latest release
- See below for details on building from source.
Align Genomes from Different Species
- See the Progressive Cactus documenation
- Please cite the Progressive Cactus paper when using Cactus. Additional descriptions of the core algorithms can be found here and here.
Align Genomes from the Same Species and Build Pangenome Graphs
- See the Minigraph-Cactus Pangenome Pipeline documenatation
- Please cite the Minigraph-Cactus paper.
Cactus uses many different algorithms and individual code contributions, principally from Joel Armstrong, Glenn Hickey, Mark Diekhans and Benedict Paten. We are particularly grateful to:
- Yung H. Tsin and Nima Norouzi for contributing their 3-edge connected components program code, which is crucial in constructing the cactus graph structure, see: Tsin,Y.H., "A simple 3-edge-connected component algorithm," Theory of Computing Systems, vol.40, No.2, 2007, pp.125-142.
- Bob Harris for providing endless support for his LastZ pairwise, blast-like genome alignment tool.
- Melissa Jane Hubiz and Adam Siepel for halPhyloP and Phast.
- Sneha Goenka and Yatish Turakhia for SegAlign, the GPU-accelerated version of LastZ.
- Yan Gao et al. for abPOA
- Heng Li for minigraph, minimap2, gfatools and dna-brnn
- Dany Doerr for GFAffix, used to optionally clean pangenome graphs.
- The vg team for vg, used to process pangenome graphs.
- The authors of Mash
Please subscribe to the cactus-announce low-volume mailing list so we may reach about releases and other announcements.
Installing Manually From Source
Cactus requires Python >= 3.7 along with Python development headers and libraries
Clone cactus and submodules
git clone https://github.com/ComparativeGenomicsToolkit/cactus.git --recursive
Create the Python virtual environment. Install virtualenv first if needed with
python3 -m pip install virtualenv.
cd cactus virtualenv -p python3 cactus_env echo "export PATH=$(pwd)/bin:\$PATH" >> cactus_env/bin/activate echo "export PYTHONPATH=$(pwd)/lib:\$PYTHONPATH" >> cactus_env/bin/activate source cactus_env/bin/activate python3 -m pip install -U setuptools pip python3 -m pip install -U . python3 -m pip install -U -r ./toil-requirement.txt
If you have Docker installed, you can now run Cactus. All binaries, such as
cactus-consolidated will be run via Docker. Singularity binaries can be used in place of docker binaries with the
--binariesMode singularity flag. Note, you must use Singularity 2.3 - 2.6 or Singularity 3.1.0+. Singularity 3 versions below 3.1.0 are incompatible with cactus (see issue #55 and issue #60).
By default, cactus will use the image,
quay.io/comparative-genomics-toolkit/cactus:<CACTUS_COMMIT> when running binaries. This is usually okay, but can be overridden with the
CACTUS_DOCKER_TAG environment variables. For example, to use GPU release 2.4.4, run
export CACTUS_DOCKER_TAG=v2.4.4-gpu before running cactus.
Compiling Binaries Locally
In order to compile the binaries locally and not use a Docker image, you need some dependencies installed. On Ubuntu (we've tested on 20.04 and 22.04), you can look at the Cactus Dockerfile for guidance. To obtain the
grep apt-get Dockerfile | head -1 | sed -e 's/RUN //g' -e 's/apt-get/sudo apt-get/g'
Progressive Cactus can be built on ARM cpus including on Mac (with packages installed via Brew), but Minigraph-Cactus is currently X86-only.
To build Cactus, run
make -j 8
In order to run the Minigraph-Cactus pipeline, you must also run
In order to toggle between local and Docker binaries, use the
--binariesMode command line option. If
--binariesMode is not specified, local binaries will be used if found in
PATH, otherwise a Docker image will be used.