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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 MetaGEAR Workflows

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 MetaGEAR Workflows for a similar analysis.

Underlying tools

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

Contact

MetaGEAR is developed at the Schirmer Lab.