MetaGEAR

MetaGEAR is an umbrella platform for high-throughput microbiome metagenomic analysis and interactive gene-function exploration. It consists of two main components:

• MetaGEAR Pipeline A Nextflow/NF-Core pipeline that streamlines end-to-end microbiome metagenomic workflows—from raw reads to functional annotation.

• MetaGEAR Web A web server enabling interactive exploration of microbial gene functions in Inflammatory Bowel Disease (IBD) and Colorectal Cancer (CRC). Results from MetaGEAR Pipeline can be uploaded for seamless integration.

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📦 MetaGEAR Pipeline

Features

• Quality control & trimming (FastQC, TrimGalore)
• Host- and contaminant-read removal (Kneaddata)
• Microbial Profiling (MetaPhlAn, HUMAnN)

Prerequisites

• Java 11+
• Nextflow 22+
• Docker or Singularity

Installation

To install the Pipeline, just run:

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

Usage

MetaGEAR requires 3 databases: Kneaddata, MetaPhlAn, HUMAnN. These can be downloaded by running the command:

metagear download_databases

To run the QC and Microbial Profiles workflows, run:

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

The input file should look like this:

sample,fastq_1,fastq_2
SAMPLE-01,/path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz
SAMPLE-02,/path/to/sample2_R1.fastq.gz,/path/to/sample2_R2.fastq.gz

🌐 MetaGEAR Web

Try it out live at: http://metagear.schirmerlab.de

MetaGEAR Web lets you:

• Search microbial gene families by sequence or functional domains
• Explore gene-level abundance changes in IBD and CRC cohorts
• Interactive filtering, search, and plots