exSimulator

exSimulator is a simulation framework for modeling host–exogenous (e.g., virus–host) chimeric structures and sequencing data.

It supports:

1. eccDNA structure simulation with corresponding long-read WGS data.
2. fusion transcript simulation with matched ONT long-read RNA-seq data.

Designed for benchmarking integration detection and fusion transcript identification tools, exSimulator provides controllable, ground-truth-aware datasets.

Overview

exSimulator is organized into two benchmarking modules:

• Genome module (eccDNA + long-read WGS)
• Transcriptome module (fusion transcript + ONT long-read RNA-seq)

Current repository status:

• Genome module is available.
• Transcriptome module interface is defined and being integrated.

Installation

1. Clone repository

git clone https://github.com/iukoi77-oas/exSimulator.git
cd exSimulator

2. Python dependencies

python3 -m pip install pandas matplotlib

3. External tools

Make sure these commands/resources are available in your environment:

• ecSimulator source tree (with src/ecSimulator.py and src/run_nanosim.py)
• excalibur
• minimap2
• samtools
• optional: pigz

Tutorials & Usage

Module A: Genome (eccDNA + long-read WGS)

Quick-start documentation:

• Genome Module README

Module B: Transcriptome (fusion transcript + ONT RNA-seq)

Quick-start documentation:

• Transcriptome Module README

Citation

If you use exSimulator in your work, please cite the project and related method paper(s).

Suggested citation format (update fields before release):

@software{exsimulator,
  title   = {exSimulator: A framework for virus-host chimeric structure and sequencing simulation},
  author  = {Your Team},
  year    = {2026},
  url     = {https://github.com/<org>/exSimulator}
}

License

This project is distributed under the MIT License. See LICENSE.