Method for detecting genomic structure variation based on nanopore sequencing

A technology for nanopore sequencing and structural variation, which is applied in the field of bioinformatics and can solve problems such as low accuracy and precision, and difficulty in structural variation.

Active Publication Date: 2019-12-20
BIOMARKER TECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0003] Most high-throughput sequencing technologies basically sequence short fragments of DNA (generally 150-300

Method used

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  • Method for detecting genomic structure variation based on nanopore sequencing
  • Method for detecting genomic structure variation based on nanopore sequencing
  • Method for detecting genomic structure variation based on nanopore sequencing

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0050] Example 1 The method for detecting structural variation based on nanopore sequencing is applied to the detection of structural variation in rice individual resequencing

[0051] Rice individual resequencing structural variation detection, including the following steps:

[0052] 1. Perform quality control on the off-machine data of nanopore sequencing, mainly including filtering adapter sequences, reads quality value lower than 7 and reads length shorter than 500bp. Based on the filtered data statistics clean data, the results are as follows:

[0053] Table 1 Clean data statistics

[0054] #DataType SeqNum SumBase N50Len N90Len MeanLen Max Len MeanQual clean data 2001147 1300993204 21490 4007 10081 211522 9.33

[0055] Note: Data type: data type; SeqNum: sequence number; SumBase: total base number; N50Len: data N50 length; N90Len: data N90 length; MeanLen: average length of reads; MaxLen: longest Reads length; MeanQual: average R...

Embodiment 2

[0065] Example 2 The method of detecting structural variation based on nanopore sequencing is applied to rice resequencing transgenic events and insertion fragment search

[0066] Rice resequencing transgenic events and insertion fragment search, including the following steps:

[0067] 1. Perform quality control on the off-machine data of nanopore sequencing, mainly including filtering adapter sequences, reads quality value lower than 7 and reads length shorter than 500bp. Based on the filtered data statistics clean data, the results are as follows:

[0068] Table 4 Clean data statistics

[0069] #DataType SeqNum SumBase N50Len N90Len MeanLen Max Len MeanQual clean data 2826773 2057904109 28822 14733 22062 207257 8.32

[0070] Note: Data type: data type; SeqNum: sequence number; SumBase: total base number; N50Len: data N50 length; N90Len: data N90 length; MeanLen: average length of reads; MaxLen: longest Reads length; MeanQual: average...

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Abstract

The present invention provides a method for detecting genomic structure variation based on nanopore sequencing, which includes performing nanopore sequencing data quality control and genomic mapping;excavating within-alignment reads and split reads information; defining structural variation and typing; and performing multi-sample data variation type integration. The method of the invention can detect the variation of mutants and wild-type materials, the variation between extremely resistant materials, transgenic events and the location of inserted fragments; can also organically integrate theresults of a large number of samples and assist in the correction of variation sites; provide rich structural variation data for natural resource groups for subsequent GWAS analysis; not only can detect common large fragment structural variations, but also have high accuracy and precision in the detection of chimeric mutations, and clusters the reads of the typed structural mutations to determinehomozygous and heterozygous structural variations.

Description

technical field [0001] The invention belongs to the technical field of bioinformatics, and specifically relates to a method based on nanopore sequencing detection and motion group structural variation, and specifically relates to nanopore sequencing off-machine data quality control, reference genome comparison, structural variation detection and final large sample size Data Integration. Background technique [0002] Structural variation of the genome (Structure Variants), usually refers to the sequence changes and positional relationship changes of large fragments on the genome, and there are rich types of variations, including large sequence insertions or deletions (Big Indel) and tandem duplications with a length of more than 50 bp (Tandem repeat), chromosomal inversion (Inversion), chromosomal translocation (Translocation), copy number variation (CNV) and more complex forms of chimeric variation. Compared with SNP (single nucleotide polymorphism), structural variation ac...

Claims

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Application Information

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IPC IPC(8): G16B30/00
CPCG16B30/00
Inventor 郑洪坤王运通李绪明邓德晶梁若冰王晶
Owner BIOMARKER TECH
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