Systematic review of next-generation sequencing simulators: computational tools, features and perspectives

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• High-throughput next-generation sequencing (NGS) generates vast genomic datasets.
• NGS simulators are essential tools for developing and validating computational methods.
• The comparative performance of existing NGS simulators is not well-understood.

Purpose of the Study:

• To conduct a comprehensive review and comparison of NGS simulators.
• To evaluate the performance of simulators across diverse sequencing techniques.
• To provide guidance for selecting appropriate simulators in genomic research.

Main Methods:

• Systematic literature review of NGS simulators.
• Categorization of simulators based on sequencing technology (DNA, metagenomics, RNA-seq, ChIP-seq, bisulfite sequencing).
• Comparative analysis of simulator features and reported performance.

Main Results:

• Identified a range of NGS simulators with varying capabilities.
• Highlighted performance differences among simulators for specific sequencing types.
• Revealed a lack of standardized benchmarks for simulator evaluation.

Conclusions:

• The choice of NGS simulator significantly impacts downstream analysis.
• Further development of standardized evaluation metrics is needed.
• This review provides a valuable resource for researchers selecting NGS simulation tools.