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BaseClear offers complete bioinformatics services and solutions for microbial profiling analysis. Standard solutions for microbial profiling include 16S and/or ITS amplicon analysis for taxonomic classification and relative frequencies. Our managers are happy to discuss the ideal workflow that best fits your needs and budget and our main drive is to make sure that your research questions are answered!

A schematic overview of a 16S-amplicon based approach: Illumina MiSeq reads are merged into overlapping pseudo-reads and subsequently aligned against a 16S database. Taxonomic classification is performed using an in-house protocol. Extended advice on the project setup and in-depth downstream analysis are provided in collaboration with our partner NIZO Food Research.


Our bioinformatics department has developed two state-of-the-art microbial profiling analysis pipelines. The 16S based amplicon analysis protocol generally involves the Illumina MiSeq sequencing platform which is capable of producing paired-end reads of length 300 nt. Alternatively also the Illumina HiSeq and PacBio SMRT platforms can be used to generate shorter and longer reads, respectively. Depending on your research question and available budget, BaseClear can offer the best possible strategy that guarantees an optimal output. In most cases Illumina MiSeq paired-end reads are generated which are merged into overlapping pseudo-reads using our bioinformatics analysis pipeline. In this manner a relatively long stretch of the 16S rRNA gene can be covered (e.g. the V3-V4 region) with single reads. Subsequently each read is aligned against a 16S rRNA gene database for taxonomic classification.

The standard output includes a comprehensive table containing all taxonomies found and their counts, but also a number of publication-ready figures which allow an easy (graphical) interpretation of the findings (e.g. a cladogram, piechart and barchart). The results can also be easily viewed and compared in an interactive manner using our unique online BaseClear metaGenome Browser (BmGB)™.

<Click here> to read more about our interactive online metaGenome Browser. 

Our 16S amplicon-based analysis protocol includes the generation of easy-to-interpret tables and figures. For example the Taxonomic pie chart displayed in the figure provides a clear overview of the taxonomic classifications and relative abundance. 

Alternatively taxonomic data can be easily (and interactively) explored with zoomable Krona pie chart (Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385.).

Delivered output:

  • Taxonomy table containing a summary of all read-annotations and their relative abundance.
  • Publication-ready figures and plots (barchart, piechart, cladogram).
  • Microbial profiling analysis report containing a summary of the 16S annotation results.
  • Free access to our online BaseClear metaGenome Browser (BmGB)™ which allows interactive analyses of the results (read more on our 'Interactive online platforms' page)

Meet Walter Pirovano!

Walter is director of the bioinformatics department and supervises our team of excellent bioinformaticians with expertise in the field of next-gen analysis and (far) beyond.

Testimonial DuPont Industrial Biosciences

The support that BaseClear has provided in the field of bioinformatics and downstream processing of next generation sequencing data has been extremely important for us. There are of course other organisations that offer next generation sequencing but that does not mean that you have everything you need. BaseClear's extra service is unique and represents one of their great strengths.

Senior Scientist


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