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Module Metagenomics

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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.

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Additional Resources

Metagenomic Analysis use case: https://www.biobam.com/metagenomic-analysis-of-two-soda-lakes-with-and-without-cyanobacterial-bloom-with-omicsbox/ .

Metagenomics Example Dataset: Download