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Assembly method and assembly device for chromosome level genome

An assembly method and chromosome technology, applied in the field of genome assembly, can solve problems such as difficult to achieve genome assembly at the chromosome level

Active Publication Date: 2022-05-10
上海诺禾致源医学检验实验室有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0007] The main purpose of the present invention is to provide a chromosome-level genome assembly method and assembly device to solve the problem that it is difficult to achieve chromosome-level genome assembly for species without Hi-C sequencing data in the prior art

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  • Assembly method and assembly device for chromosome level genome
  • Assembly method and assembly device for chromosome level genome
  • Assembly method and assembly device for chromosome level genome

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Experimental program
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Embodiment 1

[0029] In this embodiment, a genome assembly method at the chromosome level is provided, such as figure 1 As shown, the assembly method includes:

[0030] S101, obtaining the known chromosome-level genome of the same species as a reference genome;

[0031] S103, comparing the contig or scaffold of the individual to be assembled with the reference genome to obtain corresponding coordinate information;

[0032] S105. Mount the contig or scaffold of the individual to be assembled to the chromosome level according to the coordinate information, and obtain the genome of the individual to be assembled at the chromosome level.

[0033] This assembly method uses the published chromosome-level genome of the same species as the reference genome, and compares the contig or scaffold-level genome of the newly tested individual (for example, using mummer) to the reference genome, so as to realize the reference of the newly tested individual. The purpose of mounting to the chromosome level...

Embodiment 2

[0048] This embodiment provides a method for mounting genome parameters to the chromosome level, such as figure 2 As shown, the specific implementation process is as follows:

[0049] 1. Use the nucmer command in mummer to compare the target genome to the chromosome-level genome, the reference sequence is the chromosome-level genome sequence, and the target genome sequence is the query sequence to obtain the comparison file.

[0050]2. Use the delta-filter command in mummer to filter the shorter alignment sequences in the alignment file to obtain the filtered alignment file.

[0051] 3. Use the show-coords command in mummer to convert the filtered alignment file into an aligned coordinate matrix file.

[0052] 4. According to the coordinate matrix file after mummer comparison, output the corrected coordinate file. Determine whether the end position of the query sequence in the comparison region is greater than the start position of the query sequence in the comparison regio...

Embodiment 3

[0064] This embodiment provides a chromosome-level genome assembly device, the assembly device includes: an acquisition module, a comparison module and a mounting module, wherein,

[0065] The obtaining module is configured to obtain the known chromosome-level genome of the same species as a reference genome;

[0066] The comparison module is configured to compare the contigs or scaffolds of the individuals to be assembled with the reference genome to obtain corresponding coordinate information;

[0067] The mounting module is configured to mount the contig or scaffold of the individual to be assembled to the chromosome level according to the coordinate information, and obtain the genome of the individual to be assembled at the chromosome level.

[0068] Optionally, the alignment module includes a mummer module.

[0069] In a preferred embodiment, the comparison module includes: a mummer module, a correction module and a deduplication module, wherein,

[0070] The mummer mod...

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Abstract

The invention provides an assembling method and an assembling device for a chromosome level genome. The assembling method comprises the following steps: acquiring a known chromosome level genome of the same species as a reference genome; comparing the contigs or scaffolds of the individuals to be assembled with the reference genome to obtain corresponding coordinate information; and according to the coordinate information, mounting the contigs or scaffolds of the to-be-assembled individuals to chromosome levels to obtain chromosome level genomes of the to-be-assembled individuals. For a species which is difficult to provide Hi-C data, the published chromosome level genome of the same species is used as a reference genome, and a contig or a scaffold level genome of a newly detected individual is compared to the reference genome, so that the aim of mounting the newly detected individual to a chromosome level with parameters is fulfilled.

Description

technical field [0001] The invention relates to the field of genome assembly, in particular to a chromosome-level genome assembly method and assembly device. Background technique [0002] Genome assembly is generally divided into second-generation sequencing data assembly and third-generation sequencing data assembly. The commonly used assembly software for second-generation sequencing data is soapdenovo. Through the combination of small fragments and large fragment data, the assembly result is a scaffold level genome; third-generation sequencing data is commonly used The assembly software is canu or falcon, and the result of the assembly is the contig level genome. Neither of the above two sequencing assembly methods can assemble the genome to the chromosome level. [0003] Hi-C (High-through chromosome conformation capture) technology is a high-throughput chromosome conformation capture technology, using the principle that the interaction strength within chromosomes is mu...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/20G16B30/10
CPCG16B30/20G16B30/10
Inventor 赵勇周勋康玲陶琳娜王静
Owner 上海诺禾致源医学检验实验室有限公司
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