Pathogen detection pipeline

With our pathogen detection pipeline we offer an efficient, fast and accurate solution to detect pathogens in a variety of sample types. Our pipeline includes false-positive adjusted species-level taxonomic analysis by shotgun metagenomics sequencing. With this pipeline we can quickly scan for pathogens in metagenome data. We detect both known and unknown pathogens. Our state-of-the-art tools deliver way to better distinguish low abundant pathogens from false positives.

Our innovative pathogen detection method is comprehensive, fast and able to detect contaminants at low abundance levels. This rapid method is assembly-free and uses specific pathogen databases and downstream analyses to check for low abundant potentially pathogenic species. Our pipeline can be used on metagenomic sequencing data from an wide array of samples.

Read our blog on validation steps

Advantages of our pathogen detection pipeline;

  • Dedicated databases covering pathogenic genera from different domains
  • The database is customizable according to the client needs
  • False-positive adjustment reduces the number of low abundance false positives
  • Fast detection of contamination
  • Detection of low abundant species
  • User friendly output table
  • Additional functional analysis to investigate the pathogenicity of the detected species

Altogether, our integrated metagenome pipeline offers a reliable approach to quickly detect pathogens. This method can replace more laborious and less precise traditional methods of pathogen detection. Get in touch with our experts to discuss the possibilities!

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Meet Eline Klaassens!

Eline joined BaseClear in 2020 as Product Manager Human Health. Eline has a strong background in human microbiome analysis, holding a PhD degree from Wageningen University in Microbial Eco-physiology of the Human Intestinal Tract. She has used multiple omics tools for profiling diversity as well as functionality of the human microbiome.

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