TEtrimmer: a tool to automate the manual curation of transposable elements

Abstract

Abstract Transposable elements (TEs) are repetitive DNA sequences that move within genomes and play important roles in gene regulation and genome evolution. Accurate TE annotation in genomes is crucial for downstream analyses but challenging due to their sequence diversity and frequent fragmentation, including the occurrence of nested copies. We here present TEtrimmer, a tool that automates and replaces key steps of traditional manual curation of TEs. TEtrimmer combines phylogenetic tree analysis with the machine learning method DBSCAN to cluster TE sequences accurately and applies a sliding-window strategy to remove poorly conserved regions of TE-derived multiple sequence alignments. TEtrimmer also provides detailed report plots and features a graphical user interface (GUI) application. Tested on the genomes of six organisms belonging to various kingdoms of eukaryotic life and three simulated genomes, TEtrimmer consistently improved the identification of intact TEs compared to the established tools EDTA and RepeatModeler2.