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Meeting Abstract

EDTA2: De Novo Transposon Annotation in Diverse TE Landscapes


Bao,  Z       
Department Molecular Biology, Max Planck Institute for Biology Tübingen, Max Planck Society;

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Ou, S., Liao, H., Lu, T., Bao, Z., Heringer, P., Dainat, J., et al. (2024). EDTA2: De Novo Transposon Annotation in Diverse TE Landscapes. In Plant and Animal Genome 31 Conference (PAG 2024).

Cite as: https://hdl.handle.net/21.11116/0000-000E-4255-8
Long-read sequencing technologies have revolutionized the field by sequencing thousands of new genomes, thus highlighting the urgent need for rapid and precise genome annotation. While the annotation of transposable elements (TEs) has benefited from various automated tools, the challenge of adapting to increasingly diverse TE landscapes remains. The Extensive De-novo TE Annotator (EDTA) was developed to deliver automated, high-quality TE annotation and has been facilitating hundreds of plant genome studies. However, opportunities for further refinement have emerged to better meet the evolving demands of the scientific community. This talk introduces EDTA2, an enhanced version of the software characterized by increased speed and versatility, and tailored to diverse TE landscapes. EDTA2 notably improves the sensitive and accurate de novo annotation of non-LTR elements, which are prevalent in vertebrate genomes. Additionally, we enhance the performance of dependent programs like TIR-Learner and AnnoSINE, facilitating their adaptation to de novo TE annotations in large-scale genomes and pangenomes.