Method and device for haploid typing and variation detection of diploid genome sequencing fragments

Abstract

A method and device for haploid typing and variation detection of diploid genome sequencing fragments. The typing method includes: aligning the CCS sequence of the third-generation sequencing fragments to a reference genome to obtain the optimally aligned sequencing fragments, and storing them in a linked list object In the structure; filter each SNP site to obtain the site corresponding to the candidate heterozygous single nucleotide polymorphism, and store it in a dictionary type variable; build a binary tree structure, and each layer of nodes corresponds to the candidate heterozygous single nucleotide polymorphism Assign values ​​to these nodes at the corresponding sites; repeatedly cut out the two sub-nodes connected to the two nodes of each layer until all the SNP information is stored in the binary tree structure, and the hybrid single nucleotide The haplotype information of the acid polymorphism is transferred to the dictionary type variable; look up the SNP information of all objects in the linked list object structure, and distinguish and record the CCS sequences corresponding to the two haplotypes according to the haplotype information. The invention greatly improves the effects of haploid typing and variation detection.

Description

technical field [0001] The invention relates to the technical field of genotyping, in particular to a method and device for haploid typing and variation detection of diploid genome sequencing fragments. Background technique [0002] After Pacific Biosciences released the first commercial third-generation sequencing platform (PacBio RS) in 2011, it successively released PacBio RSⅡ and so on. Third-generation sequencing can generate sequencing fragments (reads) up to 60kb in length. Technical details can be found in the article (Eid, John, et al. Real-time DNAsequencing from single polymerase molecules. Science 323.5910(2009):133-138.). [0003] Taking the human genome as an example, the distance between adjacent heterozygous SNPs is about 1kb-1.5kb. The short sequences obtained by using the second-generation sequencing platform are mostly 100bp, which cannot span most heterozygous single nucleotide polymorphism sites. Statistical analysis and population analysis are require...

AI Technical Summary

Problems solved by technology

[0005] Aiming at the problems of poor accuracy, low sensitivity, and short typing region length of the existing diploid genome haploid typing technology, the present invention provides a method and device for haploid typing of diploid genome sequencing fragments , to cluster the sequenced fragments in any region of the diploid genome to distinguish the sequenced fragments corresponding to the two haplotypes to achieve the purpose of haplotype typing

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