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EDTA

Description

edta website

This package is developed for automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries.

For the initial search of TE candidates, LTRharvest, LTR_FINDER_parallel, and LTR_retriever are incorporated in this package to identify LTR retrotransposons; GenericRepeatFinder, TIR-Learner, and MITE-Hunter are incorporated in this package to identify TIR transposons (a subclass of DNA transposons); HelitronScanner is incorporated in this package to identify Helitron transposons (a subclass of DNA transposons); and finally RepeatModeler is used to identify any TEs missed by these structure-based programs (such as SINEs and LINEs).

The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.

Environment Modules

Run module spider edta to find out what environment modules are available for this application.

Environment Variables

  • HPC_EDTA_DIR - installation directory
  • HPC_EDTA_BIN - executable directory

Citation

If you publish research that uses edta you have to cite it as follows:

Ou, S., Su, W., Liao, Y., Chougule, K., Agda, J. R. A., Hellinga, A. J., Lugo, C. S. B., Elliott, T. A., Ware, D., Peterson, T., Jiang, N., Hirsch, C. N., & Hufford, M. B. (2019). Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology, 20(1), 275. https://doi.org/10.1186/s13059-019-1905-y

Categories

phylogenetics