SISTEM

Documentation | Installation | Quickstart | Wrapper

SISTEM (SImulation of Single-cell Tumor Evolution and Metastasis) is a software package and mathematical model for simulating tumor evolution, cell migrations, and DNA-seq data at single-cell resolution. SISTEM simulates tumor populations under somatic clonal selection using an agent-based model. It can be used to simulate ground truth cell or clonal lineages and migration graphs while generating CNA profiles, SNV profiles, bulk-seq read counts, single-cell read counts, and allele-specific scDNA-seq reads. You can find the documentation and a number of examples by following the links appearing below the title. For a quick and easy start to using SISTEM, check out the Quickstart guide for an introduction and the Wrapper for end-to-end simulations.

If you would like to learn more about the underlying algorithms used in SISTEM, please see the paper below.

SISTEM can be cited as follows:

SISTEM: simulation of tumor evolution, metastasis, and DNA-seq data under genotype-driven selection
Samson Weiner and Mukul S. Bansal
Bioinformatics, 41(12), btaf634, 2025