A genome-wide association analysis method based on multiple genome comparisons and next-generation sequencing data

Abstract

The invention discloses a genome-wide association analysis method based on multiple genome comparisons and second-generation sequencing data. Step 1: use comparison software to compare a reference genome and a de novo assembled genome file; Insert into the position of the reference genome, and update the annotated gene position or structure in the reference genome. Step 3: If there are multiple de novo assembled genomes, update the reference genome iteratively in turn; Step 4: Use the comparison software to compare the next-generation sequencing data of the sample. For the updated reference genome, step 5, collect the demarcation point position information of all structural variations of all samples into a set, and construct a population genotype. Step 6: perform functions according to the associated sites and the updated reference genome annotation file The present invention realizes the genome-wide association analysis using structural 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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