**Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline** Transposable elements (TEs) are significant components of eukaryotic genomes and play crucial roles in evolutionary processes. However, TE annotation and characterization remain challenging, especially for non-specialists, due to the complexity of existing pipelines. Current automated TE annotation methods often suffer from issues such as fragmented and overlapping annotations, leading to erroneous estimates of TE count and coverage, and poor capture of 5' and 3' ends of repeat models. To address these challenges, the authors present Earl Grey, a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Earl Grey combines widely used library-based and de novo TE annotation tools, with TE consensus and annotation refinements. It aims to generate high-quality TE libraries, annotations, and analyses for eukaryotic genome assemblies. Key features of Earl Grey include: - **User-Friendliness**: Available via GitHub, Bioconda, Docker/Singularity containers, and web browser via gitpod. - **Parallelization**: Utilizes multiple CPU threads to reduce runtime. - **Robustness**: Capable of handling large genomes and diverse genomic contexts. - **Quality Control**: Includes a post-annotation process using RepeatCraft to merge overlapping annotations and improve TE divergence estimates. The performance of Earl Grey was evaluated using nine simulated genomes and the *Drosophila melanogaster* genome. Results showed that Earl Grey outperformed widely used methods such as EDTA and RepeatModeler2 in terms of Matthew’s correlation coefficient (MCC) scores, correct classification rates, and TE consensus sequence lengths. Earl Grey also addressed issues with overlapping and fragmented annotations, leading to more accurate and comprehensive TE annotations. Overall, Earl Grey provides a comprehensive and fully automated TE annotation toolkit that is user-friendly and robust, making it a valuable resource for researchers studying TE biology and evolution.**Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline** Transposable elements (TEs) are significant components of eukaryotic genomes and play crucial roles in evolutionary processes. However, TE annotation and characterization remain challenging, especially for non-specialists, due to the complexity of existing pipelines. Current automated TE annotation methods often suffer from issues such as fragmented and overlapping annotations, leading to erroneous estimates of TE count and coverage, and poor capture of 5' and 3' ends of repeat models. To address these challenges, the authors present Earl Grey, a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Earl Grey combines widely used library-based and de novo TE annotation tools, with TE consensus and annotation refinements. It aims to generate high-quality TE libraries, annotations, and analyses for eukaryotic genome assemblies. Key features of Earl Grey include: - **User-Friendliness**: Available via GitHub, Bioconda, Docker/Singularity containers, and web browser via gitpod. - **Parallelization**: Utilizes multiple CPU threads to reduce runtime. - **Robustness**: Capable of handling large genomes and diverse genomic contexts. - **Quality Control**: Includes a post-annotation process using RepeatCraft to merge overlapping annotations and improve TE divergence estimates. The performance of Earl Grey was evaluated using nine simulated genomes and the *Drosophila melanogaster* genome. Results showed that Earl Grey outperformed widely used methods such as EDTA and RepeatModeler2 in terms of Matthew’s correlation coefficient (MCC) scores, correct classification rates, and TE consensus sequence lengths. Earl Grey also addressed issues with overlapping and fragmented annotations, leading to more accurate and comprehensive TE annotations. Overall, Earl Grey provides a comprehensive and fully automated TE annotation toolkit that is user-friendly and robust, making it a valuable resource for researchers studying TE biology and evolution.