A transparent and unified Bash pipeline for processing raw sequencing data from epigenetics experiments.

Epi-Flow takes your raw FASTQ files and produces analysis-ready alignments, peaks, signal tracks, and a comprehensive quality control report. It is designed to be readable, reproducible, and portable, running on anything from a personal workstation to an HPC cluster.

Unified Workflow: A single, intelligent script handles multiple chromatin profiling assays with protocol-aware parameter adjustments.

White-Box Design: Written in pure Bash for ultimate transparency. No complex wrappers or containers—you can read and understand every step of the analysis.

Comprehensive QC: Integrates FastQC, Picard, deepTools, and more, culminating in a single, interactive MultiQC report to give you full confidence in your data.

Portable & Reproducible: Runs anywhere Bash is available. With strict error handling and detailed logging, your analyses are robust and entirely reproducible.

A quick two-step guide to get up and running.

git clone https://github.com/zqzneptune/epi-flow.git
cd epi-flow
chmod +x epi_flow.sh

All installation instructions, tutorials, and parameter guides have been moved to our dedicated documentation site. This is the best place to start.

The pipeline is run from the command line. Here is a typical command for an ATAC-seq experiment:

./epi_flow.sh \
    -a atac \
    -n MySample_ATAC_Rep1 \
    -1 path/to/MySample_R1.fastq.gz \
    -2 path/to/MySample_R2.fastq.gz \
    -x /path/to/genomes/hg38 \
    -g 2913022398 \
    -b /path/to/genomes/hg38-blacklist.v2.bed \
    -o ./results/MySample_ATAC_Rep1

For detailed parameter explanations and examples for other assays, please see the Usage section in our documentation.

We welcome contributions! Please see the Support & Contributions page in our documentation for details on how to report issues or submit a pull request.

This project is licensed under the MIT License. See the LICENSE file for details.