TrEMOLO : accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches Mohamed, M. /Sabot, François Varoqui, M. Mugat, B. Audouin, K. Pelisson, A. Fiston-Lavier, A. S. Chambeyron, S. Genome Software Transposable element calling Long-read DNA sequencing Nanopore sequencing Transposable element allelic frequency Haplotypes Structural variation Transposable Element MOnitoring with LOng-reads (TrEMOLO) is a new software that combines assembly- and mapping-based approaches to robustly detect genetic elements called transposable elements (TEs). Using high- or low-quality genome assemblies, TrEMOLO can detect most TE insertions and deletions and estimate their allele frequency in populations. Benchmarking with simulated data revealed that TrEMOLO outperforms other state-of-the-art computational tools. TE detection and frequency estimation by TrEMOLO were validated using simulated and experimental datasets. Therefore, TrEMOLO is a comprehensive and suitable tool to accurately study TE dynamics. TrEMOLO is available under GNU GPL3.0 at https://github.com/Drosophila GenomeEvolution/TrEMOLO. 2023 text https://www.documentation.ird.fr/hor/fdi:010087606 fdi:010087606 Mohamed M., Sabot François, Varoqui M., Mugat B., Audouin K., Pelisson A., Fiston-Lavier A. S., Chambeyron S.. TrEMOLO : accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches. 2023, 24 (1), 63 [20 ] EN