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.
To install the Pipeline, just run:
curl -L http://get-metagear.schirmerlab.de | bash
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
Try it out live at: http://metagear.schirmerlab.de
MetaGEAR Web lets you: