Method and devices of using third-generation sequence to optimize second-generation assembly result

Abstract

The invention discloses a method and devices of using a third-generation sequence to optimize a second-generation assembly result. The method includes: obtaining the second-generation assembly resultand a third-generation assembly result; using the third-generation assembly result as a reference sequence, and aligning the second-generation assembly result to the reference sequence; obtaining sequences which are in contig sequences of both sides of gap sequences of the second-generation assembly result and are aligned or not aligned to the reference sequence; substituting for gap sequences bysequences, which are not aligned to the reference sequence, to obtain the new gap sequences; and using third-generation data to carry out hole filling on the new gap sequences to obtain an optimized second-generation assembly result. The method can improve accuracy of genome assembly indicators and splicing.

Description

technical field [0001] The present invention relates to the technical field of sequencing sequence assembly, in particular to a method and device for optimizing second-generation assembly results using third-generation sequences. Background technique [0002] At present, genome assembly is mainly based on next-generation sequencing data obtained from the whole genome shotgun (WGS) Illumina sequencing platform. Its main features are high sequencing throughput, fast speed, high accuracy, low cost, and the ability to measure different insertions DNA fragment libraries of large size, especially DNA fragment libraries larger than 1k. This sequencing method has a good application effect in the assembly of simple genomes and some relatively complex genomes. When the average sequencing depth is sufficiently deep, it can basically guarantee the accuracy of the assembly results and the integrity of the genome. Therefore, next-generation sequencing is The current mainstream sequencing...

AI Technical Summary

Problems solved by technology

However, due to the shortcomings of Pacbio sequencing, such as high sample requirements, low sequencing yield, high sequencing cost, and high single-base error rate, the development of whole-genome assembly with third-generation data is greatly restricted.

However, to improve the accuracy of sequencing, a high data multiplier is required to correct base errors, and a high data multiplier needs to bear high sequencing costs, which is a big challenge for the assembly of large genomes

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