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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 to address these two points has become increasingly easier and cheaper.

Metagenomic sequencing and analyses have a remarkably large application domain that includes fundamental research and biomedical sciences, as well large industries such pharma and food production. Although the end goal and therefore specific questions of each application area differ, two fundamental questions that have to be answered remain the same: “what species are there?” and “what are they doing?” BaseClear provides a complete answer for each of these questions.

For '16S metagenomics' please refer to our Microbial diversity analysis page. 


Our state-of-the-art shotgun metagenomics analysis pipeline covers all aspects of metagenomic analysis starting from improving the quality of reads to the generation of tables that describe the abundance of different functional units, such as KEGG KOs and pathways, across different samples. We use an in-house, improved implementation of the MOCAT2 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. As a final step, we use a highly accurate and robust method called MetaPhlAn2 (Truong et al., 2015) to characterise the taxonomic profile of metagenome sample(s). These results are then summarised (in tables) and visualised (in cladograms) per sample and per project to accelerate the interpretation of results by our clients.

BaseClear uses an improved implementation of the widely-used MOCAT2 metagenomic analysis suite.

Delivered output:

  • 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).
  • 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.

Cladograms per sample and per project are created using MetaPhlAn2 and GraPhlAn to summarise the taxonomic profile of samples and projects. 


While metagenomics 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. 

Meet Tom van den Bogert!

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


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