metaFun : pipeline for metagenomic data analysis

A scalable and agile analysis pipeline for metagenomic big data with fast and unified Functional searches.

Quick Start

Installation

conda create -c bioconda -c conda-forge -n metafun bioconda::metafun
conda activate metafun

If you have mamba, you can install metaFun with mamba

mamba create -c bioconda -c conda-forge -n metafun metafun

Download databases

metafun -module DOWNLOAD_DB

Run analysis

metafun -module RAWREAD_QC  -i input_reads/

Documentation 📖

https://metafun-doc.readthedocs.io/en/latest/index.html

metaFun pipeline flowchart

Support & Contact

metaFun is actively maintained with ongoing feature development and bug fixes. There is no restriction to use this program.

If you have any questions, feature requests, or encounter issues, feel free to reach out:

• GitHub Issues: https://github.com/aababc1/metaFun/issues
• Email: aababc1@yonsei.ac.kr
• Slack: Join our workspace

When reporting bugs, please include your OS, the module/step where the error occurred, and relevant log files (.nextflow.log, .command.log).

📚 Citation

If you use metaFun in your research, please cite:

Lee HG, et al. (2026). metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches. Gut Microbes, 17(1). https://doi.org/10.1080/19490976.2025.2611544

BibTeX

```bibtex @article{lee2026metafun, title={metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches}, author={Lee, Hyeon Gwon and others}, journal={Gut Microbes}, volume={17}, number={1}, year={2026}, publisher={Taylor bibtex @article{lee2026metafun, title={metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches}, author={Lee, Hyeon Gwon and others}, journal={Gut Microbes}, volume={17}, number={1}, year={2026}, publisher={Taylor \& Francis}, doi={10.1080/19490976.2025.2611544} } Francis}, doi={10.1080/19490976.2025.2611544} } ```