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.

RepeatExplorer2 是计算管道的新版本，它使用基于图形的下一代测序读数聚类来表征真核生物中的重复 DNA。聚类算法通过使用相对少量的短序列读取来促进任何基因组中的重复识别，管道中的其他工具对识别的重复进行自动注释和量化。该管道集成到 Galaxy 平台中，该平台为脚本执行和结果文档提供了一个用户友好的 Web 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、串联重复的识别和分析结果的增强可视化。这里，我们概述了 RepeatExplorer2 工作流程，并提供了将其应用于 (i) 单个物种的从头重复识别，(ii) 一组物种的重复序列比较分析，(iii) 开发用于细胞遗传学实验的卫星 DNA 探针的程序(iv) 基于 ChIP-seq 数据鉴定着丝粒重复序列。每个程序大约需要 2 d 才能完成。RepeatExplorer2 可在 https://repeatexplorer-elixir.cerit-sc.cz 获得。