TrEMOLO : Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches

Transposable Element MOnitoring with LOng-reads (TrEMOLO) is a new software combining assembly- and mapping-based approaches to robustly detect genetic elements called transposable elements (TE) that are able to multiply within their host genome. Using high or low quality reference genomes, TrEMOLO could detect most of the TE insertions segregating at various frequencies in a population. Benchmarking with simulated data revealed that TrEMOLO compares, or even outperforms, the other computational tools available. Detection and frequency estimation of some TE insertions were also experimentally validated. Taken together, TrEMOLO appears as a suitable tool for accurately working on the TE dynamic.