SISTEM documentation

SISTEM is an open-source Python package for simulating tumor growth, metastasis, and DNA-seq data under genotype-driven selection. It can be used to generate allele-specific copy number aberration (CNA) profiles, single-nucleotide variant (SNV) profiles, bulk-sequencing read counts, single-cell allele-specific read counts, and single-cell DNA sequencing reads, in addition to ground truth clone trees, single-cell lineage trees, and migration graphs. This makes SISTEM ideal for benchmarking methods for mutation detection, phylogenetic inference, and migration history inference. Additionally, SISTEM provides a variety of customizable selection models and migration models, making it a suitable framework for other applications such as estimating parameters from real datasets.

This manual offers instructions for installing and using SISTEM and contains example workflows. You can find an overview of the key steps in the quickstart guide and a complete list of parameters here. SISTEM is implemented as an API for high customization, but users can also use the SISTEM wrapper for easy end-to-end simulation workflows. If you would like to learn more about the underlying algorithms used in SISTEM, please see our paper (yet to be posted).

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

Under Review

Contents:

Getting started

• Installation
• Quickstart

API core and features

• Selection models
• Migration models
• Growth and lineage simulation
• DNA-seq reads/counts
• Parameters and defaults
• Output file information

Tutorials and examples

• Generating single-cell CNA profiles and cell tree
• Generating bulk profiles and clone tree
• Studying distribution of migration patterns
• Generating synthetic scDNA-seq reads