Abstract
ABSTRACTBackgroundTransposable 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.ResultsUsing 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.ConclusionsEarl 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.
Publisher
Cold Spring Harbor Laboratory