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!

Human microbiome specialist Eline Klaassens joined BaseClear to use her expertise as Product Manager Human Health. “I’ve always had a strong interest in sustainability and human health. Many people have health problems related to gut dysbiosis. Through my studies, I’ve learnt a lot about the gut microbiome and I’d like to use my knowledge to improve people’s wellbeing through applications developed with microbial genomics,” she comments. Eline advises clients about genomics analyses for expert projects for clinical trials and the food industry. "As a human microbiome expert, customers value my contribution to interpretation of the analyses to support their projects. I make an important contribution to the success of their research due to my specialised academic background,” she notes.

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