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:

Cite This

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

More References

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:

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

Project Pages

If you publish a Snakemake workflow, consider to add 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 3.5.2 with the minimum required Snakemake version. You can also change the style.