StaG mwc

The StaG metagenomic workflow collaboration (mwc) is a Snakemake implementation of a general metagenomic analysis workflow intended for microbiome research. It started out as a joint project between The Center for Translational Microbiome Research (CTMR) at Karolinska Institutet in Stockholm and Fredrik Bäckhed’s research group at Sahlgrenska in Gothenburg, and has since evolved into the default workflow for metagenomics analyses used at CTMR.


Authors:Fredrik Boulund

This is the documentation for StaG-mwc, version 0.7.0, last updated Jun 13, 2023. The documentation is available online at

StaG-mwc is published as open source under the MIT license and you are encouraged to download, use, and help improve the project by contributing code modifications as pull requests back to the project’s Github repository.


If you want to contribute to the development or submit bug fixes, have a look at the contributing guidelines in the file in the Github repository.

Citing StaG-mwc

If you find StaG-mwc useful and publish something using StaG-mwc, please cite:

Fredrik Boulund, et al. (2018).
StaG-mwc: StaG metagenomics workflow collaboration.

Also consider citing all of the tools that were run as components in specific the StaG-mwc workflow used in your analysis.

Indices and tables