MSI: strain-level pathogen detection from nanopore metagenomic sequencing data

Metagenomic sequencing is currently a common method of pathogen detection, capable of detecting all known and unidentified strains in a sample. Recently, nanopore sequencing has become a promising tool for rapid pathogen detection due to its rapid sequencing and long reads. However, identifying pathogens within a species is not easy for nanopore sequencing data due to the high sequencing error rate. To this reason, we developed the Metagenomic Strain Identification (MSI) tool, which can obtain species-specific readings and accurately screen candidate strains by using pan-genome method, thus overcoming the problems related to large reference genomic databases. Through experiments, we have verified that MSI can accurately identifies pathogen strains in samples in the presence of interfering strains.