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A Tutorial of EDTA: Extensive De Novo TE Annotator

Part of the Methods in Molecular Biology book series (MIMB,volume 2250)

Abstract

Transposable elements (TEs) are important contributors to genome structure and evolution. With the growth of sequencing technologies, various computational pipelines and software programs have been developed to facilitate TE identification and annotation. These computational tools can be categorized into three types based on their underlying approach: homology-based, structural-based, and de novo methods. Each of these tools has advantages and disadvantages. In this chapter, we introduce EDTA (Extensive de novo TE Annotator), a new comprehensive pipeline composed of high-quality tools to identify and annotate all types of TEs. The development of EDTA is based on the benchmarking results of a collection of TE annotation methods. The selected programs are evaluated by their ability to identify true TEs as well as to exclude false candidates. Here, we present an overview of the EDTA pipeline and a detailed manual for its use. The source code of EDTA is available at https://github.com/oushujun/EDTA.

Key words

  • Transposable elements
  • TE annotation
  • De novo TE identification
  • TE computational pipeline

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Acknowledgments

We thank all the authors of the EDTA paper [8]. We also thank the Iowa State University High-Performance Computing facility for assistance with the storage and processing of large datasets. This research is supported by the USDA National Institute of Food and Agriculture Hatch project number IOW05282 (TP, WS), by State of Iowa funds (TP, WS), and by the NSF Plant Genome Research Program grant IOS-1744001 (MBH, SO). The authors declare there is no competing financial interest.

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Correspondence to Thomas Peterson .

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Su, W., Ou, S., Hufford, M.B., Peterson, T. (2021). A Tutorial of EDTA: Extensive De Novo TE Annotator. In: Cho, J. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 2250. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1134-0_4

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_4

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