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Metagenomics-based pathogen analysis method, analysis device, equipment and storage medium

A technology of metagenomics and analysis methods, applied in sequence analysis, informatics, biostatistics, etc., can solve the problems of mNGS standardization obstacles, mNGS experiment repeatability, result reliability and interpretation accuracy, and achieve faster data The effect of analyzing time, improving reference meaning and interpretability, and preventing missed detection

Pending Publication Date: 2020-11-17
SUZHOU GENEWORKS TECH CO LTD
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  • Description
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  • Application Information

AI Technical Summary

Problems solved by technology

[0003] Although mNGS has achieved good results in related applications, to provide a "one-stop" mature solution, traditional mNGS still has deficiencies in experimental repeatability, reliability of results, and accuracy of interpretation, which poses a threat to the standardization of mNGS. obstacle

Method used

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  • Metagenomics-based pathogen analysis method, analysis device, equipment and storage medium
  • Metagenomics-based pathogen analysis method, analysis device, equipment and storage medium

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Effect test

Embodiment 1

[0126] 1. Metagenome sequencing

[0127] On August 9, 2019, the bronchoalveolar lavage fluid of 5 patients with chronic bronchitis was collected. After microbial nucleic acid extraction, metagenomic sequencing was performed using illumina HiSeq X to obtain off-machine sequencing data.

[0128] First, the update module will update the required database resources, organize and write them into the microbial reference sequence database and the pathogen information database, and record the update information in the local log file. Then, analyze according to the following steps.

[0129] 2. Automatic identification of sequencing data

[0130] The sequencing data is in FASTQ format. Each sequence in the FASTQ format file consists of four lines. The first line starts with the @ symbol, which is the sequence header information, the second line is the base sequence, and the fourth line is the quality value corresponding to each base. A typical FASTQ sequence of the data set of this ex...

Embodiment 2

[0159] Such as Figure 17 As shown, using the above-mentioned pathogen analysis method of the present invention and the traditional mNGS method (including the comparison method based on Diamond, the method based on Kraken software and the method based on Kaiju software) to detect a sample of known theoretical microbial composition, the results show that, The analytical method of the present invention is superior in reliability and accuracy of results. In the figure, the horizontal axis represents different detection methods, and the vertical axis represents the abundance of detected species.

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Abstract

The invention relates to a metagenomics-based pathogen analysis method and device, equipment and a storage medium. According to the metagenomics-based automatic pathogen analysis method provided by the invention, on one hand, the flow and tools of a data analysis method are integrated and optimized, and the pathogen identification process is standardized, so that the data analysis time can be greatly shortened, the clinical detection period can be shortened, and rapid detection can be realized; and on the other hand, a platform effectively distinguishes pathogenic bacteria from background bacteria by establishing a microorganism reference sequence database and a pathogen information base and comprehensively evaluating parameters and evidence grades, so that missing detection caused by non-coverage can be effectively prevented, and the reference significance and interpretability of clinical detection results are further improved.

Description

technical field [0001] The invention relates to the technical field of bioinformatics, in particular to a metagenomics-based pathogen analysis method, analysis device, equipment and storage medium. Background technique [0002] Metagenome sequencing (metagenomic next-generation sequencing, mNGS) is a method for comprehensively analyzing the genetic material (DNA and RNA) of microorganisms and hosts from patient samples, and is applied to the diagnosis of various infectious diseases, pathogenic microorganisms in disease and healthy states analyze. Its detection throughput is high, and its targets cover almost all potential pathogens, which is very suitable for discovering new pathogens and unknown sources of infection. mNGS has been recognized in related fields for comprehensive and rapid detection of all potential pathogens in samples without purification and culture. At the same time, mNGS has higher pathogen identification sensitivity and is less affected by antibiotics. ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/10G16B40/00
CPCG16B30/10G16B40/00
Inventor 张鑫磊王勇强陈俊如
Owner SUZHOU GENEWORKS TECH CO LTD
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