Background: Rapid and accurate pathogen detection is important for effective control of infectious diseases. However, traditional pathogen culture methods have a very long detection time, as well as high rates of false-positive and false-negative results. Third generation sequencing (TGS) technology brings the new possibility of being used as a pathogen detection method. However, the practicability of a pathogen detection report based on TGS is still lacking. There is also a lack of professional and accurate report interpretation. Results: Here, we report on the development of a pathogen detection and analysis tool (NPIP) based on third generation nanopore sequencing technology. We also prove the practicability of nanopore sequencing and NPIP analysis tools in emergency and clinical pathogen detection by demonstrating its use in a practical case. Conclusions: This platform provides an effective, convenient, and fast analysis tool for clinicians and public health personnel to more successfully apply TGS in pathogen detection.