What is MetaGEAR
MetaGEAR is built at the Schirmer Lab as an integrated bioinformatics platform for microbiome research. It connects three things that usually live apart — a pipeline, a CLI to drive it, and a web portal for querying bacterial genes across published cohorts — under one consistent design.
Three components
MetaGEAR Workflows — the pipeline
A Nextflow / nf-core pipeline that performs:
- Quality control & decontamination with Kneaddata and TrimGalore
- Taxonomic profiling with MetaPhlAn
- Functional profiling with HUMAnN
- Gene-centric analysis, with optional contig catalog assembly
Outputs follow a consistent, documented schema designed to be easy to post-process.
MetaGEAR Tools (CLI) — the wrapper
A small command-line tool (metagear) that handles installation, database setup, configuration, and workflow execution. It detects your hardware, installs the matching pipeline release, and runs workflows behind one-word subcommands. The Nextflow learning curve, gone.
MetaGEAR Explorer — the web portal
A web app and REST API for querying curated catalogs of microbial genes by sequence (BLAST), Pfam domain, or by exploring Metagenomic Species Pangenomes (MSPs), across 24 metagenomic cohorts covering IBD, colorectal cancer, and healthy controls. Free, hosted, no installation, available at metagear-explorer.schirmerlab.de.
What’s inside Explorer today
- 33M+ gene families across all cohorts
- 9,053 stool samples uniformly processed
- 13,795 species pangenomes with gene catalogs
Where it’s going
The platform is actively developed. New cohorts are added as they’re curated; new components will be folded in as they mature. If you want to be notified, the news page is the running log.
Citing MetaGEAR
The platform is described across multiple publications — see the Cite & contact page for the right citation depending on what you used.