Method and system for detecting macro virus group in sample

A macro virus, in-sample technology, applied in the field of macrovirome detection in samples, can solve the problems of low virus sequence integrity, low virus sequence quality, short contigs, etc., to improve the identification sensitivity and accuracy, and improve the sensitivity. and accuracy, wide range of effects

Active Publication Date: 2022-03-01
广东美格基因科技有限公司
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  • Application Information

AI Technical Summary

Problems solved by technology

[0004] (1) The existing virus sequence database is incomplete, and a large number of new viruses have not been sequenced, resulting in low sensitivity and accuracy of virus sequence identification;
[0005] (2) The contigs generated based on the next-generatio

Method used

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  • Method and system for detecting macro virus group in sample
  • Method and system for detecting macro virus group in sample
  • Method and system for detecting macro virus group in sample

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0066] Embodiment 1 detects the method for the macrovirus group in the sample

[0067] 1. Sample processing

[0068] Divide the samples into 2 parts, and carry out the experimental processing on the second-generation and third-generation sequencing platforms respectively, as follows:

[0069] 1. Next generation sequencing

[0070] 1) Firstly, total DNA was extracted by phenol-chloroform extraction. After the nucleic acid was extracted, two instruments, Thermo NanoDrop 2000 and Qubit, were used to measure the concentration and quality of the nucleic acid respectively;

[0071] 2) DNA fragments are purified and eluted by the magnetic bead method, and the ends of the fragments are repaired;

[0072] 3) Add adapters and amplify the DNA fragments to construct a sequencing library;

[0073] 4) Use the Illumina Novaseq platform for metagenomic sequencing of PE150. After the sequencing is off the machine, perform data format conversion and index splitting on the original bam file ...

Embodiment 2

[0113] Embodiment 2 detects the system of the macrovirus group in the sample

[0114] This embodiment provides a system for implementing the method for detecting macroviruses in samples in Embodiment 1, such as figure 1 shown, including:

[0115] The sequencing data storage module is used to obtain and store the second-generation sequencing data and the third-generation sequencing data of the samples to be tested;

[0116] The assembly module is connected with the sequencing data storage module, and is used for mutual correction and mixed assembly of the second-generation sequencing data and the third-generation sequencing data to obtain mixed assembly contigs, and is used to separately assemble the third-generation sequencing data to obtain Nanopore contigs;

[0117] The virus identification and annotation module, connected with the assembly module, is used to compare and annotate the mixed assembly contigs, obtain candidate virus contigs and non-virus contigs, and perform s...

Embodiment 3

[0120] Example 3 Human stool samples were subjected to metagenomic sequencing and analysis

[0121] 1. Sample processing

[0122] After the sample was divided into two parts according to the method of Example 1, the second-generation metagenomic sequencing and the third-generation metagenomic sequencing were performed respectively.

[0123] 2. Sequencing data analysis

[0124] According to the method of Example 1, the second-generation sequencing data volume of the sample is about 10Gb bases, and the third-generation sequencing data volume is about 6Gb bases. After removing the human host sequence, the remaining 9.2Gb of the second-generation data and 5.64Gb of the third-generation data. The mixed assembly of the second-generation and third-generation quality control data obtained 230,000 contigs, with a total of 512.8Mb bases; and the separate assembly of the third-generation quality control data obtained more than 2,000 contigs, with a total of 74.1Mb bases (Table 1).

[...

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Abstract

The invention discloses a method for detecting a macro virus group in a sample, and belongs to the technical field of metagenome analys.The method comprises the steps that second-generation sequencing data and third-generation sequencing data of a to-be-detected sample are mutually corrected and mixed and assembled to obtain mixed and assembled contigs, and the third-generation sequencing data are independently assembled to obtain Nanopore contigs; further, the mixed assembly contigs and the Nano-virus contigs are respectively subjected to comparison and annotation, so that candidate virus contigs, non-virus contigs and Nano-virus contigs are obtained, and the candidate virus contigs, the non-virus contigs and the Nano-virus contigs are subjected to comparison and annotation; and finally, carrying out clustering analysis on the three data sets, carrying out further comprehensive analysis according to a clustering result, supplementing missing virus sequences, and correcting a species annotation result to obtain a more sensitive, accurate and comprehensive virus identification result.

Description

technical field [0001] The invention belongs to the technical field of metagenomic analysis, and in particular relates to a method and system for detecting macroviruses in a sample. Background technique [0002] With the development of metagenomics, more and more studies have proved that viruses play a key role in different ecosystems, so it is very necessary to analyze viruses on metagenomic data. [0003] In recent years, viral metagenomics technology based on high-throughput sequencing, with its timeliness and high-throughput advantages, has enabled people to perform microbial sequencing on different types of samples and study a large number of non-culturable viruses. Current metagenomic sequencing methods mainly include next-generation sequencing (Next-generation Sequencing) and third-generation sequencing technologies. Second-generation sequencing is widely used in the field of viral metagenomics due to its high throughput and high accuracy; while the nanopore single-m...

Claims

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Application Information

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IPC IPC(8): G16B30/10G16B30/20
CPCG16B30/10G16B30/20
Inventor 林德春陈江金桃张智闵詹太平蒋华
Owner 广东美格基因科技有限公司
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