Method, system, storage medium and device for annotating macro virus group original sequencing data short-read sequence

A technology of sequencing data and macro viruses, applied in the field of bioinformatics, can solve the problems of long cycle, high cost, hindering scientific research progress, etc., and achieve the effect of simple and automatic operation, low demand for computing resources, and saving turnaround time

Pending Publication Date: 2022-02-25
SOUTHWEST UNIVERSITY FOR NATIONALITIES
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Problems solved by technology

[0005] Since many microbiological researchers or clinical workers do not have bioinformatics knowledge, and many grassroots laboratories do not have servers, most sequence alignment programs such as metaWRAP, drVM, and VirMAP need to run on the Linux platform and require high computing resources , that is, the annotation and extraction of macrovirome se

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  • Method, system, storage medium and device for annotating macro virus group original sequencing data short-read sequence

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[0031] The technical solutions of the present invention will be clearly and completely described below in conjunction with the accompanying drawings. Apparently, the described embodiments are part of the embodiments of the present invention, but not all of them. Based on the embodiments of the present invention, all other embodiments obtained by persons of ordinary skill in the art without making creative efforts belong to the protection scope of the present invention.

[0032]In the description of the present invention, it should be noted that the terms belonging to "center", "upper", "lower", "left", "right", "vertical", "horizontal", "inner", "outer" etc. The indicated direction or positional relationship is based on the direction or positional relationship described in the drawings, and is only for the convenience of describing the present invention and simplifying the description, rather than indicating or implying that the device or element referred to must have a specifi...

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Abstract

The invention discloses a method, a system, a storage medium and a device for annotating a macro virus group original sequencing data short-read sequence. Based on a windows system, the method comprises the following steps: acquiring original sequencing data, decompressing the original sequencing data and extracting the short-read sequence, generating a short-read sequence data set, and calling a blastn program to compare the data set into a database; keeping the optimal comparison result of each short read sequence, removing the result with poor comparison quality in the optimal comparison results, and then adding a virus name according to the gene id; and based on the script library, counting the number of the short read sequences annotated to each virus seed, calculating the standard deviation of the short read sequences of each virus seed on the comparison position of the genome, extracting the corresponding short read sequence according to the annotated virus seed, and outputting a fasta data set. According to the method, localization and portability of macro virus group original data annotation are achieved, and researchers without bioinformatics background knowledge can use the method conveniently.

Description

technical field [0001] The present invention relates to the field of bioinformatics, in particular to a method, system, storage medium and device for annotating short-read sequences of macrovirome raw sequencing data. Background technique [0002] The human microbiome (human microbiome), known as the second genome of the human body, is a general term for the genetic material carried by all microorganisms on the surface of the human body (Sender R, et al, 2016). Countries around the world attach great importance to this emerging field and start For example, the International Human Microbiome Alliance was initiated by the French Agricultural Research Institute in 2005 and officially established in 2008; in 2008, the Human Microbiome Project (Human Microbiome Project) was launched by the National Institutes of Project, HMP) (Methé Barbara A, et al, 2012); and the "Metagenomics of Human Intestinal TractMetaHIT" project launched by the European Union in 2008. Under its seventh fr...

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Application Information

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IPC IPC(8): G16B20/20
CPCG16B20/20
Inventor 周昱行汤承岳华
Owner SOUTHWEST UNIVERSITY FOR NATIONALITIES
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