This git repository holds shared code for the analysis of Next Generation Sequencing data related to gene regulation: ChIP-seq, RNA-seq, and related technologies.

It was developed as part of the France Genomique Workpackage 2.6: Gene expression regulation.

One of the key goals is to ensure portability and re-usability of the code.

We have chosen to use the Snakemake workflow management system[1] in order to build reproducible and flexible NGS analysis pipelines.



  1. Köster, Johannes and Rahmann, Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.

User guide and reference

Indices and tables