Get started

Two paths. Pick the one that matches what you have.

I have a biological question

A protein or nucleotide sequence. A Pfam domain. A specific MSP. You want to know where it shows up across published microbiome cohorts.

Use MetaGEAR Explorer. No installation, no setup, no data needed of your own. Currently indexing 24 cohorts spanning IBD, colorectal cancer, and healthy controls.

Sequence ──► BLAST    ──► hits across cohorts, with sample metadata
Domain   ──► Browse   ──► every gene with that Pfam domain
MSP      ──► Explore  ──► all genes in that species pangenome

Open Explorer →

I have my own sequencing data

Paired-end shotgun metagenomic reads. You want quality-controlled, taxonomically profiled, functionally annotated outputs — on your own machine or HPC.

Use the MetaGEAR Pipeline + MetaGEAR Tools (CLI).

Check prerequisites:
- Java 17+
- Nextflow 25+
- Docker or Singularity

Install MetaGEAR Tools (the CLI):

curl -L https://get-metagear.schirmerlab.de | bash

Download reference databases (one-time):
Terminal window
```
metagear download_databases
```

Prepare a samplesheet (samples.csv):

sample,fastq_1,fastq_2
SAMPLE-01,/path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz

Run a workflow:

metagear qc_dna --input samples.csv
metagear microbial_profiles --input samples.csv

Or run a preset, which chains several workflows in dependency order and reuses what each produces, so nothing is recomputed:

metagear profiles   --input samples.csv --outdir results/   # profiles only, no assembly
metagear genomes    --input samples.csv --outdir results/   # gene catalog, MAGs, pangenomes
metagear microbiome --input samples.csv --outdir results/   # everything, viruses included

Full reference lives in the metagear-tools repository.

Not sure which?

The What is MetaGEAR page explains how the components fit together. Or open an issue and we’ll point you in the right direction.