New generation sequencing copy number variation simulation method based on state transition model

A technology for copy number variation and state transfer, applied in the field of copy number variation

Active Publication Date: 2017-05-17
XIDIAN UNIV
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[0004] The purpose of the present invention is to provide a next-generation sequencing copy number variation simulation method based

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  • New generation sequencing copy number variation simulation method based on state transition model

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[0053] In order to make the object, technical solution and advantages of the present invention more clear, the present invention will be further described in detail below in conjunction with the examples. It should be understood that the specific embodiments described here are only used to explain the present invention, not to limit the present invention.

[0054] The application principle of the present invention will be described in detail below in conjunction with the accompanying drawings.

[0055] Such as figure 1 As shown, the copy number variation simulation method for next-generation sequencing based on the state transition model provided by the embodiment of the present invention includes the following steps:

[0056] S101: Design of CNV simulation algorithm and state transition model;

[0057] S102: Design of CNA simulation algorithm and state transition model;

[0058] S103: Generate the Profile file based on the Illumina sequencing platform. The core step is to ...

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Abstract

The invention discloses a new generation sequencing copy number variation simulation method based on a state transition model. The method comprises the steps that a copy number variation simulation algorithm is adopted; the state transition model is added to the simulation algorithm, and after the variation simulation, a sequence generation part is added; the copy number variation comprises germ cell copy number variation and somatic cell copy number variation; a Profile file based on an Illumina sequencing platform is generated; an ASCii code of a reads declarative part of an fq file is converted to a quality value of a basic group, and the corresponding method is that 33 is subtracted from the ASCii code of a corresponding character; the fa file obtained after the variation simulation and the generated profile file serve as input, and a read length is set, and multi-thread and sequence generation algorithms are used for generating and outputting the final fq file. According to the new generation sequencing copy number variation simulation method based on the state transition model, the biological variation simulation is more credible, the functions are complete and the data is true.

Description

technical field [0001] The invention belongs to the technical field of copy number variation, and in particular relates to a simulation method for copy number variation of next-generation sequencing based on a state transition model. Background technique [0002] Copy number variation is caused by rearrangement of the genome, generally refers to the increase or decrease of the copy number of large genome fragments with a length of more than 1kb, mainly manifested as deletion and insertion at the submicroscopic level. Copy number variation is an important part of genome structural variation (SV), and its site mutation rate is much higher than that of SNP (Single nucleotide polymorphism), which is one of the important pathogenic factors of human diseases. According to different places of occurrence, copy number variation can be divided into germ cell copy number variation (CNV) and somatic copy number variation (Copy number alteration, CNA). cell. CNVs have genetic effects, ...

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Application Information

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IPC IPC(8): G06F19/12
CPCG16B5/00
Inventor 高美虹袁细国张军英杨利英李杰白俊
Owner XIDIAN UNIV
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