Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a powerful tool for investigation the genome-wide distribution of DNA binding protein and their modifications. Yet, the computational analysis of Next-Generation Sequencing datasets is still a bottleneck for most of the experimental researchers. Most often, this type of analysis require multiple steps i.e. read quality control, mapping to a reference genome, peak calling, annotation and functional enrichment analysis that are performed by various tools e.g. fastp (S. Chen, Zhou, Chen, & Gu, 2018), bowtie2 (Langmead & Salzberg, 2012) or samtools (Li et al., 2009) only to name a few. These various tools require different software dependencies and can have different software versions and/or incompatibilities which might impair the analysis reproducibility. Here we provide a complete, user-friendly and highly customized ChIP-seq analysis pipeline for paired-end (Illumina) data based on the Snakemake workflow manager (Koster & Rahmann, 2012).