We live in a planet that is dominated by microbial communities. Exploring the diversity, composition and functional capacity of these communities is essential not only for obtaining a more complete description of the biosphere, but also for finding out how they can be utilised to improve our quality of life. Since the arrival of next-generation sequencing, studying metagenomic communities has become increasingly easier and cheaper. In all metagenomics studies two fundamental questions need to be answered: “what species are there?” and “what are they doing?”. BaseClear offers complete solutions to answer each of these questions.

Metagenomics sequencing analysis

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 the metagenome 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.


  • A de novo metagenome 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.
Flow chart of the metagenomics analysis pipeline from BaseClear


While metagenome analysis provides a wealth of knowledge with respect to the functional potential of the sampled microbial community, it does not provide information about which of these functions are expressed. The latter can be achieved by metatranscriptomics and starts with the extraction of RNA. As the extracted RNA predominantly consists of non-coding RNAs (e.g. ribosomal RNA) that do not give information about functional expression, an rRNA depletion step is performed. This is followed by library preparation and paired-end sequencing on the HiSeq Illumina platform. BaseClear offers complete solutions for metatranscriptomic research and applications. Please contact our Product Specialist Metagenomics (Tom van den Bogert) to discuss your project in detail.

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Meet Tom van den Bogert!

Tom is responsible for metagenomics and microbial profiling projects, which are based on our next generation sequencing technologies, and the development of related approaches.

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