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Third-generation sequencing sequence correction method based on local graph

A technology of local map and base sequence, applied in sequence analysis, special data processing applications, instruments, etc., can solve the problems of slow speed and low correction accuracy.

Inactive Publication Date: 2017-10-03
ZHONGSHAN OPHTHALMIC CENT SUN YAT SEN UNIV
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Problems solved by technology

[0005] This patent aims at the problems of slow speed and low correction accuracy of current third-generation sequencing sequence correction methods, and designs a three-generation sequencing sequence correction system and method based on local graphs

Method used

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  • Third-generation sequencing sequence correction method based on local graph
  • Third-generation sequencing sequence correction method based on local graph
  • Third-generation sequencing sequence correction method based on local graph

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Embodiment 1

[0068] Based on the pairwise comparison results, the correction method of the third-generation sequencing sequence based on the local graph is implemented in the following manner to complete a large number of three-generation sequencing sequence corrections. The detailed design process is as follows:

[0069] Filtering of pairwise comparison results: Filter all pairwise comparison results according to the 1-1 rule. Filtering records can eliminate the influence of repeated subsequences and wrong read information on the correction results. Filter the remaining pairwise comparison results and divide them into volumes. Each volume contains 200,000 pairwise comparison results records of sequencing sequences, and the comparison information in the volume is sorted according to the number of sequencing sequences to facilitate the concentration of each sequencing sequence record. It is convenient for subsequent correction processing. The specific method is as follows:

[0070]Based on...

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Abstract

The invention relates to a third-generation sequencing sequence correction method based on a local graph and a system of the third-generation sequencing sequence correction method. The system comprises a two-two comparison module, a multi-sequence comparison module, a correction operation comparison module, a correction operation classification module, a consistent-area base position correction and complex-area local graph base sequence correction module and a module sequence correction division and defusion processing module, the two-two comparison module is connected with a single molecule real-time sequencing database and a nanopore sequencing database, and the single molecule real-time sequencing database and the nanopore sequencing database are input into the two-two comparison module separately. The precision of the third-generation sequencing sequence correction method and system can reach 99%, and the speed is 7-10 folds that of current application software.

Description

technical field [0001] The present invention relates to a three-generation sequencing (PacBio SMRT and Oxford nanopore sequencing) sequencing sequence error correction method, in particular to a local graph-based three-generation sequencing sequence correction method. Background technique [0002] The current three-generation sequencing technology mainly includes the single molecule real-time sequencing (single molecule, real-time, SMRT) sequencing technology of PacBio Company and the nanopore (Nanopore) sequencing technology of Oxford Nanopore Company. Compared with the second-generation sequencing technology, the third-generation sequencing data has the characteristics of a very long read length (or sequencing sequence) (long read, about 10-15kb on average) and no GC bias in the sequencing sequence. There are many defects in the second-generation sequencing technology, which makes it widely used in the market: In terms of genome sequencing, researchers have used the sequen...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22
CPCG16B30/00
Inventor 肖传乐
Owner ZHONGSHAN OPHTHALMIC CENT SUN YAT SEN UNIV
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