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title: "Module Metagenomics"
canonical: "https://help.biobam.com/space/OUM3/3675863587/Module%20Metagenomics"
format: markdown
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The Metagenomics Module of OmicsBox enables the seamless combination and integration of all essential steps for a comprehensive microbiome data analysis in a flexible and user-friendly manner. Users can create custom pipelines tailored to their individual analysis strategies. Quality Control And Assessment : Use FastQC and Trimmomatic for performing quality control on your samples, filtering reads, and removing low-quality bases. Taxonomic Classification:  Identify Bacteria, Archaea, Fungi, Protozoa, and Viruses down to strain level with Kraken 2. Gain insights from rich visualizations and test for the differential abundance of taxa. Metagenomic Assembly:  Choose between MetaSPAdes and MEGAHIT to assemble large datasets easily and fast in the cloud. Gene Prediction:  Use FragGeneScan for plain reads and Prodigal for assembled data to identify and extract possible genes and proteins. Functional Analysis:  Obtain high-throughput functional annotations with EggNOG-Mapper and PfamScan. Visual comparison of results is supported, along with differential abundance testing of functions. Metagenomics Module Menu Additional Resources Metagenomic Analysis use case:   . Metagenomics Example Dataset:  Download