dcHiChIP: A comprehensive Nextflow-based pipeline for multiscale analysis of chromatin architecture from HiChIP data

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This Zenodo record provides an archival release of dcHiChIP, a modular and scalable Nextflow DSL2 workflow for comprehensive analysis of HiChIP data, corresponding to the version used in the manuscript “dcHiChIP: A comprehensive Nextflow-based pipeline for multiscale analysis of chromatin architecture from HiChIP data”. dcHiChIP enables reproducible end-to-end processing of HiChIP data from raw sequencing reads to multiscale characterization of chromatin architecture. The workflow integrates read alignment and quality filtering, peak calling, chromatin loop detection, multi-resolution contact matrix generation, TAD/CCD identification, A/B compartment and sub-compartment analysis, chromatin stripe detection, functional genomic annotation, motif enrichment, reproducibility assessment, aggregate peak analysis, and three-dimensional genome modeling. The workflow is implemented in Nextflow DSL2 and supports containerized execution using Docker, Singularity, and Apptainer, facilitating reproducible deployment across local computing systems, high-performance computing clusters, and cloud environments. This archive is intended to provide a permanent, citable snapshot of the software version and associated resources used for the analyses reported in the manuscript. Project repository: https://github.com/SFGLab/dcHiChIPDocumentation: https://sfglab.github.io/dcHiChIP/

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