Abstract：
The ever decreasing cost of Next-Generation Sequencing coupled with the emergence of efficient and reproducible analysis pipelines has rendered genomic methods more accessible. However, downstream analyses are basic or missing in most workflows, creating a significant barrier for non-bioinformaticians. To help close this gap, we developed Cactus, an end-to-end pipeline for analyzing ATAC-Seq and mRNA-Seq data, either separately or jointly. Its Nextflow-, container-, and virtual environment-based architecture ensures efficient and reproducible analyses. Cactus preprocesses raw reads, conducts differential analyses between conditions, and performs enrichment analyses in various databases, including DNA-binding motifs, ChIP-Seq binding sites, chromatin states, and ontologies. We demonstrate the utility of Cactus in a multi-modal and multi-species case study as well as by showcasing its unique capabilities as compared to other ATAC-Seq pipelines. In conclusion, Cactus can assist researchers in gaining comprehensive insights from chromatin accessibility and gene expression data in a quick, user-friendly, and reproducible manner.
摘要：
下一代测序的成本不断降低，加上高效和可重复的分析管道的出现，使得基因组方法更容易获得。然而,在大多数工作流中，下游分析是基本的或缺失的，为非生物信息学家创造了一个巨大的障碍。为了帮助缩小这个差距，我们开发了仙人掌,用于分析ATAC-Seq和mRNA-Seq数据的端到端管道，无论是单独还是联合。其Nextflow-,容器-,和基于虚拟环境的体系结构确保高效和可重复的分析。仙人掌预处理原始读取，在条件之间进行差异分析，并在各种数据库中进行富集分析，包括DNA结合基序，ChIP-Seq结合位点,染色质状态，和本体论。我们展示了仙人掌在多模态和多物种案例研究中的实用性，并展示了其与其他ATAC-Seq管道相比的独特功能。总之,仙人掌可以帮助研究人员从染色质可及性和基因表达数据中获得全面的见解，用户友好，和可重复的方式。
