HPD-Kit: A Comprehensive Toolkit for Pathogen Detection and Analysis

TengCheng Que ^1,2,3 Wen Li ^4,5,6 Zhining Zhang ⁷ Yunlin He ⁷ Kangming He ⁷ Hong Qiu ^4,7 Juan Huang ⁷ Zhiwei Lu ⁷ Chunlan Jiang ⁷ Yongjian Huang ⁷ Hui Huang ⁷ Qiuyu Wu ² Panyu Chen ⁸ Yanling Hu ^4,5,6* Wenjian Liu ^9*

• ¹ Faculty of Data Science, City University of Macau, Taipa, Macao, Macao, SAR China
• ² School of Basic Medicine, Youjiang Medical University for Nationalities, Baise, Guangx, China
• ³ Guangxi Zhuang Autonomous Terrestrial Wildlife Rescue Research and Epidemic Diseases Monitoring Center, Guangxi, China., Nanning, China
• ⁴ Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi Zhuang Region, China
• ⁵ Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China., Nanning, China
• ⁶ Key Laboratory of Biological Molecular Medicine Research (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China., Nanning, China
• ⁷ Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China., Nanning, China
• ⁸ Guangxi Zhuang Autonomous Terrestrial Wildlife Rescue Research and Epidemic Diseases Monitoring Center, Nanning, 530025, Guangxi, China., Nanning, Guangxi Zhuang Region, China
• ⁹ Faculty of Data Science, City University of Macau,999078 Macau, China, Macau, China

Unbiased metagenomic sequencing (mNGS) plays a crucial role in the diagnosis of infectious diseases and epidemiological surveillance. However, accurate analysis of mNGS data requires to possess specialized programming and bioinformatics knowledge, posing a significant challenge for many clinicians. To lower the barrier of analysis, we developed HPD-Kit (Henbio Pathogen Detection Toolkit), a tool focused on the detection and analysis of human and animal pathogens, accompanied by a corresponding pathogen database for use in conjunction with the toolkit. This paper details the construction of the HPD-Kit pathogen database, bioinformatics pipeline, and performance evaluation. Validation results with simulated datasets demonstrates that HPD-Kit maintains a considerable detection accuracy even at low pathogen abundance. Its application to clinical datasets demonstrates the ability to identify a greater number of pathogens. Additionally, HPD-Kit provides an open-source software package and a web-based analysis interface, enabling one-click analysis to facilitate clinical and public health applications.