# Citing and Citations

This section gives instructions on how to cite Snakemake and lists citing articles.

## Citing Snakemake

When using Snakemake for a publication, please cite the following article in you paper:

Mölder, F., Jablonski, K.P., Letcher, B., Hall, M.B., Tomkins-Tinch, C.H., Sochat, V., Forster, J., Lee, S., Twardziok, S.O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., Nahnsen, S., Köster, J., 2021. Sustainable data analysis with Snakemake. F1000Res 10, 33.

This “rolling” paper will be regularly updated when Snakemake receives new features.

### More References

The initial Snakemake publication was:

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

Another publication describing more of Snakemake internals:

Köster, Johannes and Rahmann, Sven. “Building and Documenting Bioinformatics Workflows with Python-based Snakemake”. Proceedings of the GCB 2012.

And my PhD thesis which describes all algorithmic details as of 2015:

Johannes Köster, “Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis”, TU Dortmund 2014

The most comprehensive publication is our “rolling” paper (see above):

Mölder, F., Jablonski, K.P., Letcher, B., Hall, M.B., Tomkins-Tinch, C.H., Sochat, V., Forster, J., Lee, S., Twardziok, S.O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., Nahnsen, S., Köster, J., 2021. Sustainable data analysis with Snakemake. F1000Res 10, 33.

### Project Pages

If you publish a Snakemake workflow, consider adding a link to the documentation with this badge to your project page.

The markdown syntax is

    [![Snakemake](https://img.shields.io/badge/snakemake-≥5.6.0-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io)

Replace the `5.6.0` with the minimum required Snakemake version. You can also change the style.