Intestinal flora metagenome database construction method and device and intestinal flora metagenome database analysis method and device

A technology of metagenomic and intestinal flora, applied in the field of building gut flora metagenomic database, can solve the problems of difficult groups, difficult to elucidate, and no gut flora metagenomic data database, etc., to achieve accurate and reliable information, It is beneficial to management and the interaction of database data

Pending Publication Date: 2020-06-09
康美华大基因技术有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, due to the independence of scientific research projects, different project data have different processing methods and processes, and the sample size has certain limitations, making it difficult to extensively evaluate the characteristics of the population, and it is difficult to find specific biomarkers (biomarkers) , it is less easy to elucidate whether the difference between different disease states is a symptom or has a mor

Method used

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  • Intestinal flora metagenome database construction method and device and intestinal flora metagenome database analysis method and device
  • Intestinal flora metagenome database construction method and device and intestinal flora metagenome database analysis method and device
  • Intestinal flora metagenome database construction method and device and intestinal flora metagenome database analysis method and device

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Embodiment 1

[0078] Glossary:

[0079] Sra2HMGA is a package file of database data preprocessing process written by Perl, which contains standard input folder input, output folder output, folder for running process (bin), process description file (readme), etc.

[0080] Phenotype.xls is a standardized sample phenotype file, and the phenotype information that does not exist in the sample is uniformly processed as NA.

[0081] kneaddata_read_count_table.tsv is the data filtering and quality control information obtained after the Fastq file analyzed by the open source software Kneaddata and then processed by the Biobakery process.

[0082] merged_abundance_table_species.txt is the species abundance information file obtained after analyzing the input Fastq file by the open source software Metaphlan2. Specifically, this file belongs to the species abundance information at the "species" level, and the species abundance information is based on Relative abundance after sample normalization.

[0...

Embodiment 2

[0117] Such as Figure 5 and Figure 6 As shown, this embodiment provides a system for constructing an intestinal flora metagenomic database, including the following modules:

[0118] Acquisition module: used to obtain the initial data resources of human intestinal flora metagenomics, the initial data resources include microbial metagenomic data and host phenotype data;

[0119] Preprocessing module: used to preprocess the acquired initial data resources, the preprocessing includes phenotypic information sorting and quality control, and abundance data acquisition;

[0120] Storage module: used to store the processed data according to the set input format to obtain the macrogene database.

[0121]The database construction method includes constructing internal storage database and public storage database, constructing database query module, constructing database data interaction system and constructing database data analysis system. The data interaction system includes data a...

Embodiment 3

[0129] Embodiment 3 discloses a computer-readable storage medium, which is used to store a program, and when the program is executed by a processor, the method for constructing an intestinal flora metagenomic database of Embodiment 1 is implemented.

[0130] Of course, a storage medium containing computer-executable instructions provided by an embodiment of the present invention, the computer-executable instructions are not limited to the above-mentioned method operations, and can also perform related operations in the methods provided by any embodiment of the present invention .

[0131] Through the above description about the implementation mode, those skilled in the art can clearly understand that the present invention can be realized by means of software and necessary general-purpose hardware, and of course it can also be realized by hardware, but in many cases the former is a better implementation mode . Based on this understanding, the essence of the technical solution ...

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Abstract

The invention discloses an intestinal flora metagenome database construction method which comprises the following steps: acquiring initial data resources of a human intestinal flora metagenome, the initial data resources comprising microbial metagenome data and host phenotype data; preprocessing the acquired initial data resources, wherein the preprocessing comprises phenotypic information arrangement and quality control and abundance data acquisition; and storing the processed data according to a set entry format to obtain a metagene database. The invention further discloses an analysis method and system based on the intestinal flora metagenome database, and a storage medium. According to the intestinal flora metagenome database construction method, screening and unified standard processing are carried out on original data, so that obtained database information is accurate, reliable and standard, and information transmission, database management and database data interaction are facilitated.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a method for constructing an intestinal flora metagenomic database, an analysis method and a device. Background technique [0002] With the development of the Human Microbiome Project (HMP) and Human Intestinal Metagenomics (MetaHIT) projects, people's understanding of intestinal flora has gradually deepened. More and more studies have shown that the intestinal flora is an important "organ" of the human body. They maintain a symbiotic or antagonistic relationship in the intestinal tract, and together form a dynamic and balanced micro-ecosystem, participating in the regulation of the body's physiological functions. Intestinal flora disorder is closely related to the health of the host, and is the source of many diseases, such as autoimmune diseases, metabolic diseases and some malignant tumors. [0003] At present, high-throughput sequencing of the genome of intestinal flora in host ...

Claims

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Application Information

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IPC IPC(8): G16B50/30G16B20/00
CPCG16B50/30G16B20/00
Inventor 许冬瑾周勇罗文廖和睿
Owner 康美华大基因技术有限公司
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