Whole genome association analysis method based on comparison of multiple genomes and next-generation sequencing data

Abstract

The invention discloses a whole genome association analysis method based on comparison of multiple genomes and next-generation sequencing data, which comprises the following steps of: 1, comparing a reference genome with a de novo assembly genome file by using comparison software; and updating the annotation gene positions or structures in the reference genomes; 3, if a plurality of de novo assembly genomes exist, sequentially iteratively updating the reference genomes; 4, comparing the next-generation sequencing data of the samples to the updated reference genome by using comparison software; 5, collecting demarcation point position information of all structural variations of all the samples into a set, constructing a population genotype; and 6, performing functional gene candidate according to the association site and the updated reference genome annotation file. According to the method, the whole genome association analysis is performed by using the structure variation genotype data.

Description

technical field [0001] The invention relates to a reference genome based on multiple genome comparisons and its annotation update, mining of sequence structure variation based on next-generation sequencing data, population genotype construction based on multi-sample genome structure variation, and genome-wide association based on structural variation genotype The analysis method, in particular to a genome-wide association analysis method based on multiple genome comparisons and next-generation sequencing data, belongs to the field of bioinformatics technology. Background technique [0002] Genome-wide association analysis is to detect the genetic variation polymorphism of multiple individuals in the whole genome range, obtain the genotype, and then conduct statistical analysis on the genotype and observable phenotype at the population level, and mine the traits related to trait variation. Gene. There are various forms of genome-wide genetic variation, such as base substitut...

AI Technical Summary

Problems solved by technology

However, there are many deficiencies in the current construction of the pan-genome strategy, and the organizational form of the pan-genome cannot be unified. Due to the variety of genome variations, it indicates that the pan-genome may not be linear. Some researchers have proposed a genome based on graph theory, but the multidimensional graph The formal pan-genome is not easy to understand, and the classic analysis software such as BWA that compares the existing second-generation sequencing data to the reference genome is only suitable for linear reference genomes; 2. In terms of whole-genome sequencing data, compared with the third-generation sequencing technology , Hi-C technology, etc. Next-generation sequencing technology has advantages in price and accuracy, and can provide effective sequencing data for mining population-wide genome structural variation; 3. Currently, there are various methods for detecting structural variation using next-generation sequencing data and linear reference genomes , including relying on sequencing coverage depth methods, paired-end sequencing methods, sequence read length segmentation methods, and assembly methods. Each method has its own characteristics, and its advantages and disadvantages coexist.

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