chrom-seek 🔬

An awesome set of epigenetic pipelines

This is the home of the pipeline, chrom-seek. Its long-term goals: to accurately call and annotate peaks, to infer cell types in cell-free samples, and to boldly quantify diferential binding or accessibility like no pipeline before!

Overview¶

Welcome to chrom-seek's documentation! This guide is the main source of documentation for users who are getting started with our bulk epigenetic pipelines.

The ./chrom-seek pipeline is composed of several interrelated sub-commands to set up and run the pipeline across different systems. Each of the available sub-commands performs different functions:

chrom-seek is an awesome set of pipelines designed specifically for cell-free ChIP-seq, bulk ChIP-seq, and bulk ATAC-seq sequencing data. It relies on technologies like Singularity¹ to maintain the highest level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by Snakemake², a flexible and scalable workflow management system, to submit jobs to a cluster.

The pipeline is compatible with data generated from Illumina short-read sequencing technologies. As input, it accepts a set of FastQ files and can be run locally on a compute instance or on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users.

Before getting started, we highly recommend reading through the usage section of each available sub-command.

For more information about issues or troubleshooting a problem, please check out our FAQ prior to opening an issue on Github.

Contribute¶

This site is a living document, created for and by members like you. chrom-seek is maintained by the members of NCBR and is improved by continuous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our GitHub repository .

Citation¶

Please note that more citation styles and releases can be found on the chrom-seek zenodo page.

If you use this pipeline, please cite it as below:

@software{routsong_2026_16921008,
  author       = {Markowitz, Tovah and
                  Routsong, Ryan and
                  Khleborodova, Asya and
                  Kuhn, Skyler},
  title        = {OpenOmics/chrom-seek},
  month        = aug,
  year         = 2026,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.16921008},
  url          = {https://doi.org/10.5281/zenodo.16921008},
}

Markowitz, T., Routsong, R., Khleborodova, A., & Kuhn, S. (2026). OpenOmics/chrom-seek [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.16921008

References¶

<sup>1. Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.
2. Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.</sup>