%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Mohamed, M.
%A Sabot, François
%A Varoqui, M.
%A Mugat, B.
%A Audouin, K.
%A Pelisson, A.
%A Fiston-Lavier, A. S.
%A Chambeyron, S.
%T TrEMOLO : accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches
%D 2023
%L fdi:010087606
%G ENG
%J Genome Biology
%@ 1474-760X
%K Genome ; Software ; Transposable element calling ; Long-read DNA ; sequencing ; Nanopore sequencing ; Transposable element allelic frequency ; Haplotypes ; Structural variation
%M ISI:000964185700001
%N 1
%P 63 [20 ]
%R 10.1186/s13059-023-02911-2
%U https://www.documentation.ird.fr/hor/fdi:010087606
%> https://horizon.documentation.ird.fr/exl-doc/pleins_textes/2023-06/010087606.pdf
%V 24
%W Horizon (IRD)
%X 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