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

Abstract

Background: Transposable elements (TEs) are found in nearly all eukaryotic genomes and are implicated in a range of evolutionary processes. Despite considerable research attention on TEs, their annotation and characterisation remain challenging, particularly for non-specialists. Current methods of automated TE annotation are subject to several issues that can reduce their overall quality: (i) fragmented and overlapping TE annotations may lead to erroneous estimates of TE count and coverage; (ii) repeat models may represent small proportions of their total length, where 5' and 3' regions are poorly captured; (iii) resultant libraries may contain redundancy, with the same TE family represented more than once. Existing pipelines can also be challenging to install, run, and extract data from. To address these issues, we present Earl Grey: a fully automated transposable element annotation pipeline designed for the user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Results: Using a simulated genome, three model genome assemblies, and three non-model genome assemblies, Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above by producing longer TE consensus sequences in non-redundant TE libraries, which are then used to produce less fragmented TE annotations without the presence of overlaps. Earl Grey scores highly in benchmarking for TE annotation (MCC: 0.99) and classification (97% correctly classified) in comparison to existing software. Conclusions: 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 aspects and tailored analyses in future releases.

Genome assembly of the edible jelly fungusDacryopinax spathularia(Dacrymycetaceae)

“…Transposable element (TE) annotation was performed by following the Earl Grey TE annotation workflow pipeline (version 1.2, https://github.com/TobyBaril/EarlGrey) (Baril et al, 2022).…”

First draft genome assembly and characterization of spongeHalisarca dujardiniireveals key components of basement membrane and broad repertoire of aggregation factors

“…Repetitive elements in the genome were analyzed using the Earl Grey pipeline 18 Resulted .gtf were assembled with TACO v0.7.3 with default settings. These TACO-produced transcript coordinates provided to PASA pipeline together with de novo and genome guided transcriptomes 19 , where only transcripts with more than 90% transcript coverage (parameter --MIN_PERCENT_ALIGNED) and 95% identity (parameter --MIN_AVG_PER_ID) to the genome were merged.…”

Genome Report: Pseudomolecule-scale genome assemblies ofDrepanocaryum sewerzowiiandMarmoritis complanata

“…Repeats and transposable elements were annotated using the Earl Grey v3.2 (Baril et al 2023(Baril et al , 2024) pipeline with default settings followed by softmasking of the repeats using the maskfasta function of bedtools. The BRAKER3 pipeline (v3.0.6) (Stanke et al 2006(Stanke et al , 2008Gotoh 2008;Iwata and Gotoh 2012;Buchfink et al 2015;Hoff et al 2016Hoff et al , 2019Kovaka et al 2019;Pertea and Pertea 2020;Brůna et al 2021;Bruna et al 2024) was used to predict gene models using mRNA and protein evidence.…”