Method and device for determining microbial species

A microbial species, microorganism technology, applied in the field of microbial detection

Pending Publication Date: 2016-10-05
BGI BIOTECH WUHAN CO LTD +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Moreover, the current clinical method has a big problem in the efficiency of pathogen detection, and cannot give the classification information of microbial colonies in the sample at one time.

Method used

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  • Method and device for determining microbial species
  • Method and device for determining microbial species
  • Method and device for determining microbial species

Examples

Experimental program
Comparison scheme
Effect test

Embodiment

[0053] A urine sample (sample name: UPUR14GY0001) of a clinical patient was obtained from the hospital, data preprocessing was performed on the data generated by sequencing, and the generated data was converted into the standard FASTQ format. It is then aligned to the host's reference genome, and those sequences that do not align and those whose similarity threshold is below the specified threshold are extracted. Then compare the extracted sequences to the four database files of bacteria, fungi, viruses, and protists to classify pathogenic microorganisms. Then each comparison result (comparison file) is deduplicated, coverage and other statistical values ​​are calculated, and finally a readable result file is generated.

[0054] The steps and processes of this detection system are integrated into a software package named UPMD (Unknown Pathogen Microorganism Detection). The operating environment of this software is the Unix / Linux operating system, and it runs through the Unix / L...

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Abstract

The invention discloses a method for determining microbial species in a sample. The method comprises the following steps: sequencing at least one part of nucleic acids in the to-be-detected sample, so as to obtain sequencing data; performing alignment of the sequencing data with a first reference sequence, wherein the first reference sequence is a known sequence which is derived from the to-be-detected sample and belongs to an individual organism category, and acquiring a read which meets at least one of (1)-(3), wherein (1) the read is not subjected to alignment with the first reference sequence, (2) the similarity, with the first reference sequence, of the read is less than a preset proportion, and (3) the read is subjected to alignment with the first reference sequence and alignment quality is lower than a threshold; and performing alignment of the obtained read with a microbial reference sequence, and determining the microbial species in the to-be-detected sample in accordance with an acquired alignment result, wherein the microbial reference sequence includes at least two of bacterium, fungus, virus and protist reference sequences. The invention also discloses a device for determining the microbial species in the sample and a method for detecting pathogenic microorganisms.

Description

technical field [0001] The present invention relates to the field of microorganism detection, specifically, the present invention relates to a method for determining the type of microorganism contained in a sample, a method for detecting pathogenic microorganisms and a device for determining the type of microorganism contained in the sample. Background technique [0002] Metagenomics (Metagenomics, hereinafter referred to as meta) is used to study the genome of uncultured microbial samples. It's fast, it's cheap, and it's expanding our understanding of the microbial world. Extracting useful information from millions of sequences is a serious challenge for bioinformatics analysis. In microorganisms with cultured samples, genome data are derived from a single clone, which is relatively easy for both sequence assembly and species classification. In the metagenomic data, the sequences are derived from heterogeneous microbial colonies, which makes the sequences noisy. [0003]...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68C12Q1/04C12M1/00
Inventor 周天亮文张纪斌杨志凯叶明芝
Owner BGI BIOTECH WUHAN CO LTD
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