Pathogenic microorganism metagenome detection method based on third-generation sequencing

Abstract

The invention discloses a pathogenic microorganism metagenome detection method based on third-generation sequencing, the method comprises the following steps: acquiring original gene detection data of third-generation sequencing of a sample, removing interference sequences, and retaining non-human data; establishing a mapping relationship between the whole species nucleic acid database and the whole species classification database; removing invalid mapping relationships in the mapping relationship set to obtain an effective mapping relationship set of the non-human source data and the whole species classification database, and performing calculation according to the effective mapping relationship set to obtain a species identification result; constructing a microorganism annotation database to obtain microorganism annotation information; constructing a microbial drug resistance database to obtain microbial drug resistance information; and obtaining a microorganism detection report according to the species identification result, the microorganism annotation information and the microorganism drug resistance information. According to the method, the non-human source data is established, the mapping result is optimized, the detection precision is improved, the accuracy of species classification in similar regions is improved, and then species are obtained through prediction and comparison of sequence results.

Description

technical field [0001] The invention relates to the technical field of biological information, in particular to a method for detecting pathogenic microorganism metagenomics based on three-generation sequencing. Background technique [0002] Pathogenic microorganisms are one of the main factors causing human diseases. In the process of diagnosing human diseases, biological tests of human samples are usually required. [0003] Metagenomics is also called microbial environmental genomics and metagenomics. It directly extracts the DNA of all microorganisms from environmental samples, constructs a metagenomic library, and uses genomics research strategies to study the genetic composition and community functions of all microorganisms contained in environmental samples. It is a new concept and method developed on the basis of microbial genomics to study microbial diversity and develop new physiologically active substances (or obtain new genes). Its main meaning is: clone the tota...

AI Technical Summary

Problems solved by technology

5) Nucleic acid-based PCR detection generally has high accuracy, and the detection speed only takes a few hours. However, due to the need to design specific primers and probes, only 10-20 species can be identified at a time, and each Species require targeted design of primers and probes

Therefore, the application of third-generation sequencing has great advantages in pathogen detection, but the sequencing accuracy of third-generation sequencing is lower than that of second-generation sequencing. These data characteristics determine that the second-generation data analysis method cannot be simply followed.

[0018] In addition, the data based on next-generation sequencing is generally based on the kmer-based algorithm for species identification due to the large amount of data. This method is less accurate in the identification of highly similar nucleic acids and can only be relatively accurately distinguished at the genus level. In order to improve the analysis speed, most processes only retain the genomic nucleic acid database of known pathogenic species that have been reported, and there are certain blind spots for the identification of pathogens that have not been reported.

Images