Cassiopeia is an end-to-end pipeline for single-cell lineage tracing experiments. The software contained here comes equipped with modules for processing sequencing reads, reconstructing & plotting trees, analyzing these trees, and benchmarking new algorithms.

You can find all of our documentation here.

We also have provided tutorials for three modules:

• processing fastqs
• reconstructing trees
• simulating trees and benchmarking

You can also find our originally describing Cassiopeia published in Genome Biology.

Free Software: MIT License

For users:

pip install git+https://github.com/YosefLab/Cassiopeia@master#egg=cassiopeia-lineage

For developers:

1. Clone the package as so: git clone https://github.com/YosefLab/Cassiopeia.git

2. Ensure that you have Python >= 3.7 installed. (Python 3.6 may still work, but is not guaranteed.) We prefer using miniconda.

3. [Optional] Make sure that Gurobi is installed. You can follow the instructions listed here. To verify that it's working correctly, use the following tests:

   • Run the command gurobi.sh from a terminal window
   • From the Gurobi installation directory (where there is a setup.py file), use python setup.py install --user

4. Install Cassiopeia by first changing into the Cassiopeia directory and then pip3 install .. To install dev and docs requirements, you can run pip3 install .[dev,docs].

To verify that it installed correctly, try running our tests with pytest.

If you've found Cassiopeia useful for your research, please consider citing our paper published in Genome Biology:

Matthew G Jones*, Alex Khodaverdian*, Jeffrey J Quinn*, Michelle M Chan, Jeffrey A Hussmann, Robert Wang, Chenling Xu, Jonathan S Weissman, Nir Yosef. (2020), [*Inference of single-cell phylogenies from lineage tracing data using Cassiopeia*](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02000-8), Genome Biology