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Transposable Elements (TEs) are repeated sequences ubiquitous in Eukaryotes that can easily represent more than half of the bases of an assembled genome. While TE activity is under tight regulation to prevent deleterious mutation, TE-derived sequences are also an important source of genomic innovation and regulatory sequences, often essential to the host survival. Thus, the identification of TE in new genomic assemblies is a crucial – yet challenging – step of the annotation process. In this workshop, I will provide a primer in TE biology and a simple pipeline for de-novo detection and annotation of TE-derived sequences. The methodology presented represents a minimal, yet state-of-the-art, approach based around RepeatModeler2 and RepeatMasker, which can be used as a precursor to gene annotation and comparative genomic analyses. We will discuss the challenges posed by TE in bioinformatics and strategies aimed to foster reproducibility, as well as the existing resources available to tackle TE-related questions (TE-hub).