Metagenomics

Our state-of-the-art shotgun metagenomics sequencing pipeline covers all aspects for metagenome analysis. This starts with the quality control of the data, and includes metagenome assembly and the generation of tables that describe the abundance of different functional units, such as KEGG KOs and pathways, across different samples. To this end, we use an in-house, improved analysis suite that includes metagenome assembly, gene prediction, gene catalogue creation and annotation, as well as abundance estimation of annotated genes and other functional units.

In addition, we use a highly accurate and robust method to deduce taxonomic profiles from metagenomics data. These results are not only summarised (in tables) and visualised (in cladograms) per sample and per project, but can also be visualized in our genome explorer to accelerate the interpretation of results by our clients.

Output for metagenomics analysis projects

• A de novo metagenomics sequencing assembly per sample.
• Gene predictions and their protein translations in FastA as well as GenBank formats.
• A non-redundant gene catalogue that is created by clustering the predicted genes (can be done both at sample and at project-level), providing an inventory of the gene content.
• Annotation of the gene catalogue with more than 10 databases and functional units including KEGG orthologous groups, modules, pathways, as well as COGs.
• Functional profiling (abundance) tables of non-redundant genes and KEGG KOs, modules, pathways, and COGs. Both raw and normalised abundances are provided.
• Taxonomic relative abundance profiles per sample and per project both in BIOM format and Excel-sheet format, accompanied by corresponding cladogram figures.