Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
Methods Mol Biol. 2021;2250:55-67. doi: 10.1007/978-1-0716-1134-0_4.
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 .
转座元件 (TEs) 是基因组结构和进化的重要贡献者。随着测序技术的发展，已经开发出各种计算流程和软件程序来促进 TE 的识别和注释。这些计算工具可以根据其基本方法分为三类：基于同源性、基于结构和从头开始的方法。这些工具各有优缺点。在本章中，我们介绍了 EDTA（广泛的从头 TE 注释器），这是一种新的综合管道，由高质量的工具组成，用于识别和注释所有类型的 TE。EDTA 的开发基于一组 TE 注释方法的基准测试结果。选择的程序根据其识别真正 TE 的能力以及排除假候选物的能力进行评估。在这里，我们介绍 EDTA 管道的概述和详细的使用手册。EDTA 的源代码可在 https://github.com/oushujun/EDTA 上获得。
