RepeatModeler2 for automated genomic discovery of transposable element families.
Proceedings of the National Academy of Sciences of the United States of America
The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly variable across species, automated TE discovery and annotation are challenging and time-consuming tasks. A critical first step is the de novo identification and accurate compilation of sequence models representing all of the unique TE families dispersed in the genome. Here we introduce RepeatModeler2, a pipeline that greatly facilitates this process. This program brings substantial improvements over the original version of RepeatModeler, one of the most widely used tools for TE discovery. In particular, this version incorporates a module for structural discovery of complete long terminal repeat (LTR) retroelements, which are widespread in eukaryotic genomes but recalcitrant to automated identification because of their size and sequence complexity. We benchmarked RepeatModeler2 on three model species with diverse TE landscapes and high-quality, manually curated TE libraries:
Institute for Systems Biology
Flynn, Jullien M; Hubley, Robert; Goubert, Clément; Rosen, Jeb; Clark, Andrew G; Feschotte, Cédric; and Smit, Arian F, "RepeatModeler2 for automated genomic discovery of transposable element families." (2020). Articles, Abstracts, and Reports. 3038.