Horizon 1 1 17 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES TrEMOLO : accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches Genome Biology 63 [20 ] Genome Software Transposable element calling Long-read DNA sequencing Nanopore sequencing Transposable element allelic frequency Haplotypes Structural variation 2023 fdi:010087606 ENG Genome Biology 1474-760X ISI:000964185700001 1 10.1186/s13059-023-02911-2 https://www.documentation.ird.fr/hor/fdi:010087606 https://horizon.documentation.ird.fr/exl-doc/pleins_textes/2023-06/010087606.pdf 24 Horizon (IRD) 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. 020 ; 122 ; 084 UR232 / UR226