RadiSeq: a single- and bulk-cell whole-genome DNA sequencing simulator for radiation-damaged cell models.

Area of Science:

• Radiation biology
• Genomics
• Computational biology

Background:

• Sequencing radiation-damaged cells offers insights into radiation action.
• Experimental sequencing is challenging, costly, and time-consuming.
• Existing tools lack simulation capabilities for radiation-damaged DNA sequencing.

Purpose of the Study:

• Develop a simulation framework for single- and bulk-cell whole genome sequencing.
• Simulate radiation-exposed Monte Carlo (MC) cell models.
• Aid radiation genomics studies and experimental design.

Main Methods:

• Developed RadiSeq, a multi-threaded C++ whole-genome DNA sequencing simulator.
• RadiSeq simulates Illumina sequencing for MC-generated radiation-damaged cell models.
• Validated RadiSeq by comparing simulated data with experimental results.

Main Results:

• RadiSeq accurately simulates whole-genome sequencing of radiation-damaged cells.
• Simulated data showed reasonable agreement with experimental data.
• The simulator is highly customizable via a single input parameter file.

Conclusions:

• RadiSeq provides a powerful tool for radiation genomics research.
• Enables complex simulations to optimize, plan, and validate radiation biology experiments.
• Advances the field by bridging simulation and experimental sequencing for radiation studies.