MetaGEAR Platform
Microbiome research, end‑to‑end.
A pipeline, a CLI, and a web portal — built at the Schirmer Lab to take shotgun metagenomes from raw reads to biological hypotheses.
Query bacterial genes against thousands of metagenomic samples.
Bring a sequence, a Pfam domain, or an MSP identifier. Get back where it shows up across uniformly-processed metagenomic cohorts covering IBD, colorectal cancer, and healthy controls — with cohort and sample metadata attached to every result.
- BLAST a nucleotide or protein sequence against cohort-wide gene catalogs.
- Browse by Pfam domain (e.g.
PF08020) to find every gene that contains it. - Explore MSPs — curated Metagenomic Species Pangenomes.
- Filter by cohort: IBD, CRC, healthy controls. Every hit traces back to its sample.
PF08020Pfam domain24msp_0023MSP browse24One Nextflow pipeline, four cohesive workflows.
Built on nf-core conventions. Take paired-end FASTQ files through quality control, taxonomic and functional profiling, and gene-centric analysis — reproducibly, on a laptop or an HPC cluster.
- QC & decontamination with Kneaddata and TrimGalore.
- Taxonomic profiling with MetaPhlAn.
- Functional profiling with HUMAnN.
- Gene-centric analysis, with optional contig catalog assembly.
- 01Database setupReference DBs · Kneaddata · MetaPhlAn · HUMAnN
- 02Quality controlTrim & decontaminate · Kneaddata · TrimGalore
- 03Microbial profilesTaxonomic & functional · MetaPhlAn · HUMAnN
- 04Gene-centric analysisOptional contig catalog assembly
Install the pipeline. Run a workflow. Skip the Nextflow learning curve.
MetaGEAR Tools is a tiny command-line wrapper that installs the pipeline, detects your hardware, manages reference databases, and runs workflows with one command.
- Hardware-aware: sets resource limits to ~80% of available CPUs and RAM.
- Version-locked: installs the matching pipeline release.
- One install command, one run command per workflow.
Cite the work that matches what you used.
MetaGEAR Explorer: rapid query of microbial genes across cohorts
The Explorer portal and its underlying gene-centric query infrastructure. Cite if you used Explorer or the API.
Gene-centric methodology for metagenomic analysis
The methodology underlying MetaGEAR Workflows’ gene-centric analysis. Cite if you used the pipeline or extended the methodology.
An applied study using MetaGEAR Workflows
A peer-reviewed study that applied the pipeline to a microbiome research question. Cite alongside the methodology paper for similar work.