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Gene variation detection method and system for multi-core processor

A multi-core processor, gene mutation technology, applied in genomics, instrumentation, sequence analysis, etc., can solve the problems of poor performance, unable to give full play to the performance advantages of modern multi-core processors, etc., to achieve rapid gene mutation detection, realize mutation Detection, high consistency effect

Active Publication Date: 2021-02-23
SHANDONG UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] The inventor found that limited by the java virtual machine mechanism and the additional overhead of the java virtual machine, many Java-based mutation detection tools, such as VarDict, are not available on many platforms The performance is not good, and the performance advantages of modern multi-core processors cannot be fully utilized, and the detection of genetic mutations cannot be quickly and accurately realized.

Method used

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  • Gene variation detection method and system for multi-core processor
  • Gene variation detection method and system for multi-core processor
  • Gene variation detection method and system for multi-core processor

Examples

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Embodiment 1

[0049] This embodiment provides a gene variation detection method for multi-core processors;

[0050] Genetic variation detection methods for multi-core processors, including:

[0051] S101: Preprocessing the input data; extracting brief comparison information expression CIGAR information from the preprocessed sequencing sequence read; the input data refers to a file obtained by comparing the sequence to be queried with a reference sequence;

[0052] S102: Modify the brief comparison information expression CIGAR information of the read sequencing sequence read; process the modified sequencing sequence read brief comparison information expression CIGAR information, and perform candidate mutations from the memory pool during the processing Data retrieval to obtain candidate mutation sets;

[0053] S103: Perform local re-alignment of the mutated genes in the candidate variation set to reduce the detection of false positive variations;

[0054] S104: Formatting the mutated genes...

Embodiment 2

[0153] This embodiment provides a genetic variation detection system for multi-core processors;

[0154] A genetic variation detection system for multi-core processors, including:

[0155] The preprocessing module is configured to: preprocess the input data; extract brief comparison information expression CIGAR information from the sequencing sequence read obtained after preprocessing; the input data refers to: compare the sequence to be queried with the reference sequence The files obtained by comparison;

[0156] The candidate variation set generation module is configured to: modify the brief comparison information expression CIGAR information of the read sequencing sequence read; process the modified sequencing sequence read brief comparison information expression CIGAR information, and process In the process, the candidate mutation data is retrieved from the memory pool to obtain the candidate mutation set;

[0157] A local re-alignment module configured to: perform loca...

Embodiment 3

[0163] This embodiment also provides an electronic device, including: one or more processors, one or more memories, and one or more computer programs; wherein, the processor is connected to the memory, and the one or more computer programs are programmed Stored in the memory, when the electronic device is running, the processor executes one or more computer programs stored in the memory, so that the electronic device executes the method described in Embodiment 1 above.

[0164] It should be understood that in this embodiment, the processor can be a central processing unit CPU, and the processor can also be other general-purpose processors, digital signal processors DSP, application specific integrated circuits ASIC, off-the-shelf programmable gate array FPGA or other programmable logic devices , discrete gate or transistor logic devices, discrete hardware components, etc. A general-purpose processor may be a microprocessor, or the processor may be any conventional processor, o...

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Abstract

The invention discloses a gene variation detection method for a multi-core processor. The gene variation detection method comprises the following steps: preprocessing input data; extracting brief comparison information expression CIGAR information from a sequencing sequence read obtained after preprocessing, wherein the input data is a file obtained by comparing a to-be-queried sequence with a reference sequence; modifying the brief comparison information expression CIGAR information of the read sequencing sequence read; processing the brief comparison information expression CIGAR informationof the modified sequencing sequence read, calling candidate variation data from a memory pool in the processing process, and obtaining a candidate variation set; carrying out local re-comparison on variant genes in the candidate variant set so as to reduce the detection of false positive variants; formatting the locally recompared variant genes, outputting the formatted variant genes to an outputfile, and resetting the data in the memory pool for repeated use.

Description

technical field [0001] The present application relates to the technical field of genetic variation detection, in particular to a multi-core processor-oriented genetic variation detection method and system. Background technique [0002] The statements in this section merely mention the background art related to this application, and do not necessarily constitute the prior art. [0003] With the development of sequencing technology, the explosive growth of a large amount of sequencing data poses a challenge to the computing power of variant detection. At present, many mutation detection tools have been proposed, such as haplotype-based GATKHaplotypeCaller, Mutect2, FreeBayes, heuristic-based methods VarDict, Lofreq, and VarScan2; deep learning-based DeepVariant, etc. [0004] The inventors found that limited by the java virtual machine mechanism and the additional overhead of the java virtual machine, many Java-based mutation detection tools, such as VarDict, perform poorly o...

Claims

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Application Information

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IPC IPC(8): G16B20/20G16B20/30G16B30/10
CPCG16B20/20G16B30/10G16B20/30
Inventor 刘卫国张浩宋红磊殷泽坤
Owner SHANDONG UNIV
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