TEvarSim: A genome simulator for transposable element (TE) variants.

Transposable element (TE) variants, the presence or absence of TE sequences such as LINE-1, Alu, SVA, and endogenous retroviruses, are a major source of genomic diversity and play critical roles in human health, evolution, and disease. As interest in TE variants grows, developing related methods and tools for detection has become increasingly important. However, rigorous benchmarking of TE variant detection methods remains limited due to the lack of accurate and scalable TE variant simulation platforms and the absence of reliable ground truth data. Here, we developed TEvarSim, a novel TE variant simulator that generates TE-containing genomic data in multiple formats, including genomes, short- and long-read sequencing data, and VCF files. TEvarSim supports both random and real-world TE insertions and deletions, including variants derived from pangenome graphs. It can rapidly simulate hundreds to thousands of synthetic chromosomes or genomes and model natural variation at the haplotype, individual, and population levels, making it well suited for large-scale studies. In addition, TEvarSim can directly compare simulated VCF files with TEs reported by TE detection tools, streamlining the benchmarking of TE genotyping methods. TEvarSim provides an all-in-one toolkit for simulating, evaluating, and improving TE variant detection, advancing our ability to accurately study TEs in health and disease in various species.