Chromatin immunoprecipitation sequencing (ChIP-seq) and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) have become essential technologies to effectively measure protein–DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples, correction of copy number variations, and integration of new downstream analysis tools. Here we present Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis (CoBRA), a modularized computational workflow which quantifies ChIP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses. CoBRA provides a comprehensive state-of-the-art ChIP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience. This enables researchers to gain rapid insight into protein–DNA interactions and chromatin accessibility through sample clustering, differential peak calling, motif enrichment, comparison of sites to a reference database, and pathway analysis. CoBRA is publicly available online at https://bitbucket.org/cfce/cobra

染色质免疫沉淀测序 (ChIP-seq) 和转座酶可及染色质高通量测序 (ATAC-seq) 已成为有效测量蛋白质-DNA 相互作用和染色质可及性的重要技术。然而，需要一个可扩展且可重复的管道，该管道包含样本之间的适当标准化、拷贝数变化的校正以及新下游分析工具的集成。在这里，我们介绍了用于可重复 ChIP/ATAC-seq 分析 (CoBRA) 的容器化生物信息学工作流程，这是一种模块化计算工作流程，可量化 ChIP-seq 和 ATAC-seq 峰区域并执行无监督和监督分析。CoBRA 提供了一个全面的、最先进的 ChIP-seq 和 ATAC-seq 分析流程，可供计算经验有限的科学家使用。这使研究人员能够通过样本聚类、差异峰值调用、基序富集、位点与参考数据库的比较以及通路分析，快速了解蛋白质-DNA 相互作用和染色质可及性。CoBRA 可在 https://bitbucket.org/cfce/cobra 在线公开获得