Earl Grey is a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. It addresses issues with existing TE annotation methods, such as fragmented and overlapping annotations and poor capture of 5' and 3' ends. Earl Grey outperforms current methods in TE annotation and classification, providing comprehensive and fully automated TE annotation tools with paper-ready summary figures and outputs in standard formats. Earl Grey has a modular format, with potential for future quality control and tailored analyses. It uses nine simulated genomes and Drosophila melanogaster annotation to demonstrate its effectiveness. Earl Grey is user-friendly, available via GitHub, Bioconda, Docker/Singularity, and a web browser. It runs on Linux systems and uses multiple CPU threads for parallel processing. Earl Grey includes steps for TE curation, annotation, and refinement, with a focus on generating accurate TE consensus sequences. It also addresses overlapping and fragmented TE annotations, improving TE count and coverage estimates. Earl Grey performs well in simulated data sets, outperforming EDTA and RepeatModeler2 in TE consensus generation and classification. It generates longer consensus sequences and improves TE annotation accuracy, making it a robust tool for TE annotation in eukaryotic genomes.Earl Grey is a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. It addresses issues with existing TE annotation methods, such as fragmented and overlapping annotations and poor capture of 5' and 3' ends. Earl Grey outperforms current methods in TE annotation and classification, providing comprehensive and fully automated TE annotation tools with paper-ready summary figures and outputs in standard formats. Earl Grey has a modular format, with potential for future quality control and tailored analyses. It uses nine simulated genomes and Drosophila melanogaster annotation to demonstrate its effectiveness. Earl Grey is user-friendly, available via GitHub, Bioconda, Docker/Singularity, and a web browser. It runs on Linux systems and uses multiple CPU threads for parallel processing. Earl Grey includes steps for TE curation, annotation, and refinement, with a focus on generating accurate TE consensus sequences. It also addresses overlapping and fragmented TE annotations, improving TE count and coverage estimates. Earl Grey performs well in simulated data sets, outperforming EDTA and RepeatModeler2 in TE consensus generation and classification. It generates longer consensus sequences and improves TE annotation accuracy, making it a robust tool for TE annotation in eukaryotic genomes.