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HPD-Kit: a comprehensive toolkit for pathogen detection and analysis
Tengcheng Que1,2,3, Wen Li4,5,6, Zhining Zhang7
1Faculty of Data Science, City University of Macau, Macau, Macau SAR, China.
Frontiers in Cellular and Infection Microbiology
|May 19, 2025
Summary
HPD-Kit simplifies pathogen detection using unbiased metagenomic sequencing (mNGS) for infectious disease diagnosis. This toolkit maintains high accuracy, even with low pathogen abundance, making mNGS more accessible for clinical and public health applications.
Area of Science:
- Bioinformatics
- Infectious Disease Diagnostics
- Genomics
Background:
- Unbiased metagenomic sequencing (mNGS) is vital for diagnosing infectious diseases and surveillance.
- Analysis of mNGS data requires specialized bioinformatics expertise, posing a challenge for clinicians.
Purpose of the Study:
- To develop an accessible tool for pathogen detection and analysis using mNGS.
- To overcome the bioinformatics barrier in mNGS data interpretation for clinical settings.
Main Methods:
- Developed HPD-Kit (Henbio Pathogen Detection Toolkit) featuring a curated pathogen database and optimized bioinformatics pipeline.
- Evaluated HPD-Kit performance using simulated datasets and clinical samples.
- Provided both open-source software and a web interface for user-friendly analysis.
Main Results:
- HPD-Kit demonstrated high detection accuracy, even at low pathogen abundances in simulated data.
- Clinical sample analysis showed superior pathogen identification compared to conventional methods.
- The web interface maintained high performance while enhancing usability.
Conclusions:
- HPD-Kit effectively lowers the bioinformatics barrier for mNGS analysis without compromising accuracy.
- The toolkit's dual open-source and web-based formats support broader clinical and public health adoption of mNGS for diagnostics.
