Hole filling method and device based on third-generation sequencing sequence

Abstract

The invention discloses a hole filling method and device based on a third-generation sequencing sequence. The method includes the following steps: comparing at least one sub-sequencing sequence contained in a third-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 to obtain at least one first extraction result; performing fine comparison on the first extraction result to obtain a second comparison result; extracting a sub-sequencing sequence located within a certain range of the at least one gap sequence from the second comparison result to obtain at least one second extraction result; assembling the at least one second extraction result to obtain a consistent sequence; and replacing an original sequence in a genome sketch with the consistent sequence, wherein the gap sequence is an unknown sequence. According to the scheme of the invention, the technical problem that in the process of performing genome hole filling on sequencing data, the process of comparing the sequencing sequence has a low speed, and large resource consumption is caused can be solved.

Description

Technical field [0001] The present invention relates to the field of biological information, in particular to a method and device for filling holes based on third-generation sequencing sequences. 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 available for assembling draft genomes, such as Velvet, ABySS, SOAPdeno, etc. Nevertheless, the assembled scaffold will contain many gap sequences, and "N" is generally used to fill in the representative. Generally speaking, because the sequence of the low coverage and repetitive region is too complicated, 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 the position sequence. Although the distance information of pair-end reads can connect contigs into longer scaffolds, it cannot solve the inherent probl...

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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