Method for de novo assembly of genome by comprehensively applying third-generation ultra-long reads and second-generation linked reads

Abstract

The invention discloses a method for high-efficiency and high-quality de novo assembly of a genome by comprehensively applying third-generation ultra-long reads and second-generation linked reads. Thethird-generation ultra-long reads are ultra-long reads generated by a third-generation sequencing technology Nanopore and PacBio which are most widely applied at present. The second-generation linkedreads are reads generated by a 10x Genomics sequencing platform. A high-quality genome sequence is assembled through high-efficiency hybrid assembly software. According to the method, the advantagesof the third-generation super-long reads and the second-generation linked reads are brought into full play and are integrated, and high-efficiency assembly software DBG2OLC and SPARC are combined, sothat the application cost of the third-generation sequencing technology is greatly reduced. The invention provides an efficient, reliable and economic method for large-scale and high-quality genome denovo assembly by applying the third-generation sequencing technology.

Description

technical field [0001] The invention relates to a method for de novo assembly of genome sequencing data, in particular to a mixed assembly method for third-generation sequencing data and second-generation sequencing data. Third-generation sequencing data are mainly ultra-long reads generated by Pacbio, Nanopore or other sequencing technologies, and second-generation sequencing data are mainly linked reads generated by 10x Genomics sequencing. Combined with the high-efficiency assembly software-DBG2OLC, the cost of sequencing and calculation (especially the application cost of third-generation sequencing technology) is greatly reduced. Provides an efficient and reliable method for large-scale, high-quality genome de novo assembly using third-generation sequencing technology Background technique [0002] With the development of sequencing technology, genome sequence information generated by genome de novo assembly is becoming more and more detailed and accurate. The 10X Geno...

AI Technical Summary

Problems solved by technology

[0004] However, the assembly problem caused by the high error rate of the third-generation sequencing technology has become an obstacle to its large-scale promotion

The error position of the third-generation sequencing data occurs randomly. This error can be corrected by increasing the sequencing coverage (Coverage), but the increase in coverage leads to an increase in sequencing data, which increases the cost of sequencing and computing.

Although Pacbio and Nanopore sequencing technologies have been successfully applied to genome de novo sequencing, high sequencing and computational costs hinder the large-scale application of third-generation sequencing technologies

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