User guide

Cassiopeia is a flexible tool for analyzing lineage-tracing data and benchmarking new algorithms. Perhaps the easiest way to get started with Cassiopeia is by following along with or tutorials. Generally, we’ll expect that you’ve already successfully installed Cassiopeia using the installation guide.

For any questions about Cassiopeia, please file an issue on Github. If you’d like to contribute a tutorial or a new algorithm, please follow our Contributing guide.

Tutorials

Preprocessing sequencing reads (FASTQs) with Cassiopeia

Cassiopeia Benchmarking Pipeline

Reconstructing trees with Cassiopeia

Plotting and visualizing trees with Cassiopeia

Contributed tutorials

Currently we have no contributed tutorials – if you are interested, check out our Contributing guide!