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bioRxiv · 10.1101/2022.06.30.498289

Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline

Baril, T. J.·Imrie, R. M.·Hayward, A.
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Abstract

Transposable elements (TEs) are major components of eukaryotic genomes and are implicated in a range of evolutionary processes. Yet, TE annotation and characterisation remains challenging, particularly for non-specialists, since existing pipelines are typically complicated to install, run, and extract data from. Current methods of automated TE annotation are also subject to issues that reduce overall quality, particularly: (i) fragmented and overlapping TE annotations, leading to erroneous estimates of TE count and coverage; (ii) repeat models represented by short sections of total TE length, with poor capture of 5 and 3 ends. To address these issues, we present Earl Grey, a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Using nine simulated genomes and an annotation of Drosophila melanogaster, we show that Earl Grey outperforms current widely-used TE annotation methodologies in ameliorating the issues mentioned above, whilst scoring highly in benchmarking for TE annotation and classification, and being robust across genomic contexts. Earl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focussed on further quality control and tailored analyses in future releases.

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Baril, T. J., Imrie, R. M., Hayward, A.. 2022-07-02. Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline. https://doi.org/10.1101/2022.06.30.498289

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