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Method and device for splitting homologous chromosomes of polyploid genome and application thereof

A homologous chromosome, polyploid technology, applied in genomics, sequence analysis, proteomics and other directions, can solve the problem of difficult to split homologous chromosomes

Active Publication Date: 2021-01-29
天津诺禾致源生物信息科技有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0007] The main purpose of the present invention is to provide a polyploid genome homologous chromosome split method, device and application thereof, to solve the problem in the prior art that it is difficult to The problem of correct splitting of homologous chromosomes

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  • Method and device for splitting homologous chromosomes of polyploid genome and application thereof
  • Method and device for splitting homologous chromosomes of polyploid genome and application thereof
  • Method and device for splitting homologous chromosomes of polyploid genome and application thereof

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Embodiment 1

[0038] In a typical embodiment of the present application, a method for splitting homologous chromosomes in a polyploid genome is provided. The method comprises: according to the comparison file obtained by comparing the HiC data with the polyploid genome sequence, calculating the interaction strength between the genome contigs and within the contig; judging the accuracy of the corresponding contig connection according to the interaction strength within each contig, and Interrupt the wrongly connected contigs; compare all the contigs in the genome after the wrong connection is interrupted, and obtain the similarity between contigs; perform all contigs according to the interaction strength between contigs and the similarity between contigs Clustering, so as to realize the splitting of homologous chromosomes in polyploid genomes.

[0039] In this method, the wrongly connected contigs are identified through the interaction strength within the contigs, and interrupted at the wrong...

Embodiment 2

[0052] The above method provides a way to split the homologous chromosomes in the genome at the contig level, so that the genome assembly of polyploids can reach the chromosome level. Therefore, in the second typical embodiment of the present application, a method for assembling polyploid genome sequences is also provided. The method for assembling utilizes the above-mentioned method for splitting homologous chromosomes to separate homologous genomes at the contig level. The contigs of the chromosomes are clustered to split the contigs that belong to different classes (the different classes here refer to different homologous chromosomes); then sort the contigs in each class (that is, each homologous chromosome) and Orientation, so as to obtain the polyploid genome sequence at the chromosome level.

[0053] This method not only does not require the diploid close relatives of the target polyploid genome and its genome annotation files, but also recognizes the internal misassembl...

Embodiment 3

[0056] This embodiment provides a detailed method for assembling a polyploid genome sequence, the above specific process is as follows figure 1 (Rounded rectangles represent input / output, right-angled rectangles represent processing operations):

[0057] (1) Use the HICUP software to compare the HIC data with the polyploid genome, and obtain the comparison file all.bam (according to the comparison file, the interaction strength within the contig and the interaction strength between contigs can be calculated).

[0058] (2) According to the comparison file all.bam, calculate the HIC interaction strength in the contig, and interrupt the contig that is obviously connected incorrectly in the polyploid genome ratio file (interrupt the genome and correct the wrongly connected contig), Get the genome after contig interruption and the corresponding bam file.

[0059](3) Combining the files obtained in step (2), cluster the contig at the level of non-homologous chromosomes (the cluster...

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Abstract

The invention provides a method and a device for splitting homologous chromosomes of a polyploid genome and application thereof. The splitting method comprises the following steps: calculating the interaction strength between genome contigs and the interaction strength in the contigs according to a comparison file obtained by comparing HiC data with a polyploid genome sequence; breaking the overlapping groups with connection errors according to the interaction strength in each overlapping group; performing mutual comparison by utilizing the interrupted overlapping groups to obtain the similarity among the overlapping groups; and clustering all the contigs according to the interaction strength among the contigs and the similarity among the contigs to realize the splitting of the homologouschromosomes of the polyploid genome. The method is used for identifying an overlapping group which is wrongly connected by using interaction strength in the overlapping group, breaking at a wrong place, clustering is carried out by identifying the similarity between the overlapping groups and utilizing the interaction strength and the similarity between the overlapping groups, so that the homologous chromosomes can be effectively split.

Description

technical field [0001] The invention relates to the field of assembly of polyploid genome sequences, in particular to a method, device and application for splitting polyploid genome homologous chromosomes. Background technique [0002] After the species genome is preliminarily assembled by assembly software, the contig or scaffold version of the genome is obtained, which can be considered as a fragmented sequence of genome chromosomes. In order to obtain a more continuous genome sequence, it is necessary to use various methods for scaffold connection, such as 10X Genomic, Bionano, HiC and other technologies, among which HiC technology can connect the contig or scaffold version of the chromosome to the chromosome level to obtain high-quality genome sequences. [0003] HiC technology generally includes steps such as formaldehyde fixation, restriction enzyme digestion, and library construction and sequencing. There are no specific primers in the whole process. Therefore, by com...

Claims

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Application Information

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IPC IPC(8): G16B30/20G16B20/10G16B40/00G06K9/62
CPCG16B30/20G16B20/10G16B40/00G06F18/23G06F18/22
Inventor 李本萍王璐王迪周勋陶琳娜
Owner 天津诺禾致源生物信息科技有限公司
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