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SnakeChunks

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.

Contact

References

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

User guide and reference

.. toctree::
    :numbered:
    :maxdepth: 3

    getting_started.rst
    gene-regulation_library.rst
    dependencies.rst
    tutorials.rst
    environments.rst
    snakemake.rst
    wiki.rst

Indices and tables

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