Cactus: a user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis

SummaryWith the recent rapid advancements in sequencing technology, the analysis of omics data has become increasingly important for biomedical research. However, many laboratories lack the time or expertise to thoroughly analyze such data. Among omics assays, ATAC-Seq (Assay for transposase-accessiblechromatin usingsequencing) and mRNA-Seq (messengerRNA sequencing) are easy and cost-effective methods that are commonly used to define chromatin accessibility and gene expression levels, respectively. Here we introduce Cactus (Chromatinaccessibility and transcriptomicsunifyingsoftware), a pipeline that streamlines the individual or integrated analysis of ATAC-Seq and mRNA-Seq data. The pipeline is written in Nextflow for efficient scaling, caching, and parallelization, and all tools are packaged in Singularity/Docker containers or conda/Mamba virtual environments for simple installation and high reproducibility. Cactus conducts preprocessing on raw sequencing reads, followed by differential analysis between conditions. Results are split into Differential Analysis Subsets (DASs) based on significance threshold, direction of change, annotated genomic regions, and experiment type. Then, Cactus computes enrichments of entries from internal (i.e., DASs) and external (i.e., ontologies, pathways, DNA binding motifs, ChIP-Seq (Chromatin immunoprecipitationsequencing) binding sites, and chromatin states) databases in DASs and presents results in barplots and customizable heatmaps. The visualization of the results is simplified by the generation of merged PDFs, merged tables, and formatted Excel tables. In conclusion, Cactus can assist researchers in gaining comprehensive insights from chromatin accessibility and gene expression data in a quick, easy, and reproducible manner.Availability and implementationCactus can be installed via Nextflow pull jsalignon/cactus. Source code and documentation are available online (https://github.com/jsalignon/cactus).Contactjerome.salignon@ki.seorchristian.riedel@ki.se