Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2
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DOI：
10.1038/s41596-020-0400-y
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发表时间：
2020-10-23
期刊：
影响因子：
14.8
通讯作者：
Macas, Jiri
中科院分区：
文献类型：
--
作者：
Novak, Petr;Neumann, Pavel;Macas, Jiri
RepeatExplorer2是一种新版本的计算流水线，它使用基于图形的下一代测序读数的聚类来表征真核生物中的重复DNA。通过使用相对少量的短序列读取，聚类算法便于在任何基因组中识别重复序列，管道内的其他工具执行已识别重复序列的自动注释和量化。该管道集成到Galaxy平台中，该平台为脚本执行和结果记录提供了一个用户友好的网络界面。与管道的原始版本相比，RepeatExplorer2提供了转座元件的自动注释、串联重复序列的识别和分析结果的增强可视化。在这里，我们概述RepeatExplorer2工作流程，并提供其在以下方面的应用程序：(I)单个物种的从头重复鉴定，(Ii)一组物种的比较重复分析，(Iii)用于细胞遗传学实验的卫星DNA探针的开发，以及(Iv)基于芯片序列数据的着丝粒重复序列的鉴定。每个程序大约需要2天才能完成。RepeatExplorer2可在https://repeatexplorer-elixir.cerit-sc.cz.上获得
RepeatExplorer2 is a novel version of a computational pipeline that uses graph-based clustering of next-generation sequencing reads for characterization of repetitive DNA in eukaryotes. The clustering algorithm facilitates repeat identification in any genome by using relatively small quantities of short sequence reads, and additional tools within the pipeline perform automatic annotation and quantification of the identified repeats. The pipeline is integrated into the Galaxy platform, which provides a user-friendly web interface for script execution and documentation of the results. Compared to the original version of the pipeline, RepeatExplorer2 provides automated annotation of transposable elements, identification of tandem repeats and enhanced visualization of analysis results. Here, we present an overview of the RepeatExplorer2 workflow and provide procedures for its application to (i) de novo repeat identification in a single species, (ii) comparative repeat analysis in a set of species, (iii) development of satellite DNA probes for cytogenetic experiments and (iv) identification of centromeric repeats based on ChIP-seq data. Each procedure takes approximately 2 d to complete. RepeatExplorer2 is available at https://repeatexplorer-elixir.cerit-sc.cz.