Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline

Area of Science:

• Genomics
• Bioinformatics

Background:

• Transposable elements (TEs) are crucial in eukaryotic genome evolution.
• Current automated TE annotation tools face challenges like fragmented/overlapping annotations and incomplete repeat models.

Purpose of the Study:

• To introduce Earl Grey, a user-friendly, automated pipeline for transposable element (TE) annotation in eukaryotic genomes.
• To address limitations in existing TE annotation methods, specifically fragmented/overlapping annotations and poor capture of TE ends.

Main Methods:

• Developed a fully automated TE annotation pipeline named Earl Grey.
• Utilized nine simulated genomes and a Drosophila melanogaster annotation for testing.
• Benchmarked Earl Grey against current TE annotation methodologies.

Main Results:

• Earl Grey significantly improves TE annotation quality by reducing fragmentation and overlap.
• The pipeline demonstrates superior capture of 5' and 3' TE ends compared to existing methods.
• Earl Grey shows high performance in TE annotation, classification, and robustness across genomic contexts.

Conclusions:

• Earl Grey offers a comprehensive, automated solution for TE annotation in eukaryotic genomes.
• The pipeline provides user-friendly features, including paper-ready figures and standard output formats.
• Its modular design allows for future expansion with additional quality control and analysis modules.