Earl Grey: A Fully Automated TE Curation and Annotation Pipeline

Overview

• Earl Grey is an automated transposable element (TE) annotation pipeline.
• Utilizes widely-used tools and a consensus elongation process for annotating new genome assemblies.

Features

• Automates TE curation and annotation.
• Combines tools with a consensus elongation process.
• Compatible with new genome assemblies.

Latest Release

• v6.0.1: Bug fixes for RepeatMasker Libraries verification.
• Docker container available.

Previous Changes

• v6.0.0: Updates to use Dfam v3.9, RepeatMasker v4.1.8, famdb v2.0.1.
• Configuration required for RepeatMasker with Dfam database.
• v5.1.1: Compatibility improvements with genome sequencing data, new readable summary tables.
• v5.0.0: Subroutines added for de novo TE detection and annotation.

Example Run

• Run through steps to identify, curate, annotate TEs.
• Recommended to use within tmux or screen sessions.
• Parameters:
  • Required: -g (genome), -s (species), -o (output directory).
  • Optional: -t (threads), -r (RepeatMasker search), -l (library), -i (iterations), etc.

Outputs

• Results in summaryFiles directory.
• High-level and family-level TE quantification tables.
• Repeat Landscapes and genome repeat content pie charts.

Installation

• Conda/Mamba:
  • conda create -n earlgrey -c conda-forge -c bioconda earlgrey=6.0.1
  • mamba create -n earlgrey -c conda-forge -c bioconda earlgrey=6.0.1
• Docker: Available for Dfam v3.9 and v3.7.
• Singularity: Preconfigured with Dfam v3.7.

Usage Without Installation

• Use via Gitpod for in-browser execution.

Acknowledgements

• Cites Baril et al. (2024) for the Earl Grey pipeline.
• Utilizes scripts from RepeatCraft and other open-source software.

Additional Resources

• GitHub Repository
• Reference Manuscript

• Important: Keep RepeatMasker and RepeatModeler updated for compatibility.
• Note: Running time depends on input genome repeat content, especially using RepeatModeler2.
• Manual configuration might be needed for advanced usage or specific installations.