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MetaGEAR

Cite & contact

MetaGEAR is described across multiple publications. Cite the work that matches what you actually used.

Publications

MetaGEAR Explorer

The Explorer portal and its underlying gene-centric query infrastructure.

MetaGEAR Explorer: rapid query of microbial genes across cohorts to support hypothesis generation in microbiome research. bioRxiv, 2026. bioRxiv preprint

Cite this if you used Explorer (web portal or API) for your research.

Gene-centric analysis methodology

The methodology behind the gene-centric analysis used by the pipeline and indexed by Explorer.

A scalable methodology for gene-centric metagenomic analysis. bioRxiv, 2025. bioRxiv preprint (10.1101/2025.09.29.679262)

Cite this if you used or extended the gene-centric analysis methodology itself.

Application study using the MetaGEAR Pipeline

A peer-reviewed study that applied the MetaGEAR pipeline to a real microbiome research question.

Nature Microbiology, 2025. Nature Microbiology article (s41564-025-02223-0)

Cite this alongside the methodology paper if you used the MetaGEAR Pipeline for a similar analysis.

The software itself

Every release is archived on Zenodo with a DOI. Cite this if you want to point at the exact software you ran, alongside the methodology paper.

Ríos, E., & Jin, S. schirmer-lab/metagear-pipeline. Zenodo. 10.5281/zenodo.22233494

That DOI always resolves to the most recent release. Each release also has its own version-specific DOI, shown on the Zenodo record — use that one when reproducibility matters.

Underlying tools

The MetaGEAR Pipeline orchestrates well-established tools — please also cite the relevant upstream methods (Nextflow, nf-core, Kneaddata, TrimGalore, MetaPhlAn, HUMAnN, BLAST, and others). The pipeline repository ships a CITATIONS.md with the full list and references.

Contact

MetaGEAR is developed at the Schirmer Lab.