Whole genome typing method based on Pacio subreads and Hi-C reads

Abstract

The invention relates to a whole genome typing method based on Pacbio subreads and Hi-C reads. The whole genome typing method comprises the following steps: 1) preparing a reference genome; 2) comparing second-generation sequencing data with the reference genome, and detecting all the SNP sites of each chromosome; 3) comparing Hi-C library building sequencing data with a reference genome, and building a linkage SNP group by adopting a combination of HapCUT2 with the SNP sites; 4) grouping the Pacbio subreads based on the MVP Block, and then respectively assembling the Pacbio subreads to finally obtain the sequence of each chromatid; and 5) performing whole genome sequencing on the parent genome, comparing a sequencing result to a chromatid sequence separated in the previous step, and dividing the chromatids into two groups according to a comparison result to correspond to male and female parent genomes. According to the method, the defect that contigs with too few restriction enzyme cutting sites cannot be assembled in the process of Hi-C data assembling is avoided, a linked SNP group is constructed from the aspect of whole genome, and then the Pacbio long reads are combined, so the error risk of typing is greatly reduced.

Description

【Technical field】 [0001] The invention relates to the field of genome assembly typing, in particular to a whole genome typing method based on Pacbio subreads and Hi-Creads. 【Background technique】 [0002] In 1985, American scientists proposed the Human Genome Project to sequence the human genome in order to obtain a complete human genome. Once the plan was put forward, it received global attention, and six countries (including China) participated in it. With great cooperation from various countries, the draft human genome was finally officially published in 2001, which also marked the arrival of the genome era. Subsequently, a series of technologies including resequencing, transcriptomics, and three-dimensional genomes have flourished, and the basis of these technologies can be attributed to the possession of high-quality reference genome sequences. At present, if a new species is studied at the molecular level, it usually starts with sequencing and assembly. [0003] How...

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Problems solved by technology

[0009] However, there are some defects in the existing typing processes. For example, HapCUT can only type mutation sites and does not involve assembly; because there are few restriction sites on short contigs, neither Falcon-Phase nor ALLHIC can accurately classify Shorter contigs typing, and the ALLHIC software needs to provide the genome assembled to the chromosome level of related species as a reference sequence

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