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Method and device for filling holes based on third-generation sequencing sequences

A sequence and sequencing technology, applied in the field of biological information, can solve the problems of slow sequence alignment and high resource consumption, and achieve the effect of improving speed and saving consumption.

Active Publication Date: 2022-05-31
BEIJING NOVOGENE TECH CO LTD
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AI Technical Summary

Problems solved by technology

[0006] Embodiments of the present invention provide a method and device for filling holes based on third-generation sequencing sequences, so as to at least solve the problem that the process of comparing sequencing sequences is very slow in the process of genome hole filling for sequencing data, resulting in high resource consumption. big technical problem

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  • Method and device for filling holes based on third-generation sequencing sequences
  • Method and device for filling holes based on third-generation sequencing sequences
  • Method and device for filling holes based on third-generation sequencing sequences

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Embodiment Construction

[0034] In the related art, only unique comparison software is adopted. The current alignment software for long sequences, fast and precise

[0039] For example, Minimap2 software can be used to quickly align third-generation sequencing reads.

[0045] For example, the second alignment software can be a bedtools tool, using the bedtools tool to compare genomes with grass

[0046] The original reads are divided into two categories: the first category is the three-generation sequencing reads that are aligned to the gap sequence within a certain range,

[0055] Optionally, step S112 includes: using a preset number of consistent sequences to replace the corresponding gap sequences.

[0059] Specifically, looking for gap sequences in the draft genome, and defining consecutive 25 or more Ns as gap sequences.

[0068]

[0070]

[0071] Through the real data test, the hole-filling effect of the application is slightly better than PBjelly, and the comparison speed can be improved by 8-10 time...

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Abstract

The invention discloses a hole-filling method and device based on a third-generation sequencing sequence. Wherein, the method includes: comparing at least one sub-sequencing sequence included in the three-generation sequencing sequence to obtain a first comparison result; extracting a sub-sequencing sequence located within a certain range of at least one gap sequence from the first comparison result, obtaining at least one first extraction result; finely aligning the first extraction result to obtain a second comparison result; extracting sub-sequencing sequences within a certain range of at least one gap sequence from the second comparison result to obtain at least one first Two extraction results; assembling at least one second extraction result to obtain a consensus sequence; using the consensus sequence to replace the original sequence in the genome draft; wherein, the gap sequence is an unknown sequence. The invention solves the technical problem that the process of comparing sequencing sequences is very slow in the process of filling holes in the genome of the sequencing data, resulting in large resource consumption.

Description

Method and device for filling holes based on third-generation sequencing sequences technical field The present invention relates to biological information field, specifically, relate to a kind of hole filling method based on the third generation sequencing sequence and device. Background technique [0002] De novo assembly has become one of the main applications of second generation sequencing (NGS) technology. Currently, there are a large number of software Can be used to assemble draft genomes such as Velvet, ABySS and SOAPdeno, among others. Nevertheless, the assembled scaffold There will be many gap sequences in it, which are generally represented by "N". In general, sequences due to low coverage and repetitive regions It is too complicated and the software cannot determine the corresponding sequence of the position during the assembly process, so it can only fill in the "N" base to represent position sequence. Although the distance information of pair-end re...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B30/10
Inventor 周义其李季张锦波蒋智李瑞强
Owner BEIJING NOVOGENE TECH CO LTD
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