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MIRFLOWZ

Welcome to the MIRFLOWZ documentation pages!

MIRFLOWZ is a generic small RNA-Seq workflow that allows users to classify and quantify miRNAs and/or isomiRs.

The workflow is developed in Snakemake, a widely used workflow management system in the bioinformatic community. MIRFLOWZ will pre-process, align, classify and quantify your bulk small RNA-seq sequencing libraries with publicly available state-of-the-art bioinformatics tools.

MIRFLOWZ notation

MIRFLOWZ uses the notation provided by miRBase (i.e., "miRNA primary transcript" for precursors and "miRNA" for the canonical mature miRNA). This implies that precursors are named "pri-miRs" across the workflow instead of pre-miR. This decision is made upon the lack of guarantee that "miRNA primary transcripts" are full pre-miR (and pre-miR only) sequences.

How does it work?

MIRFLOWZ requires Conda to install the basic dependencies. Each individual step of the workflow runs either in its own Apptainer container or in its own Conda virtual environment.

Once the installation is complete, you fill in a config.yaml file with parameters and a samples.tsv file with sample-specific information. You can easily trigger MIRFLOWZ by making a call to Snakemake with the appropriate parameters.

MIRFLOWZ can be executed in different systems or High Performance Computing (HPC) cluster.

How to cite

If you use MIRFLOWZ in your work, please kindly cite the following Zenodo entry:

zavolanlab/mirflowz: v0.10.0 (v0.10.0). Iris Mestres-Pascual, Alex Kanitz, & Mihaela Zavolan. (2025). Zenodo. https://doi.org/10.5281/zenodo.17120595

Reach out

Contributing

We always welcome and duly acknowledge open source contributors, for MIRFLOWZ or any other of our projects. Simply follow our onboarding instructions and please mind our Code of Conduct. If you have any questions, do not hesitate to shoot us an email.

Acknowledgements

Zavolab Biozentrum, University of Basel