Method and system for assembling genome sequence

Abstract

The invention discloses a method and a system for assembling a genome sequence. High-precision short segment sequence data obtained by a second-generation sequencing technology and long segment sequence data obtained by single-molecule real-time sequencing are combined together to assemble a genome sequence, so that the assembly efficiency and accuracy can be improved. The method comprises the following steps: (1) sequencing a sample by utilizing the second-generation sequencing technology to obtain a high-precision short segment sequence; (2) splicing the high-precision short segment sequence to obtain a high-precision frame diagram; (3) sequencing a sample which has the same source with the sample by utilizing a single-molecule sequencing technology to obtain three generations of sequencing data; (4) comparing the three generations of sequencing data in the frame diagram to obtain detailed contrast information of the three generations of sequencing data and the frame diagram; (5) clustering the three generations of sequencing data and constructing a genome frame by utilizing the detailed contrast information, and correcting the genome frame to obtain a fine genome map.

Description

technical field [0001] The invention relates to the technical field of biological information, in particular to a method and system for assembling genome sequences. Background technique [0002] Illumina's next-generation sequencing technology, with its high energy and accuracy, has become the preferred platform for many scientific research sites. At present, its average read length is 100bp-300bp. Due to its high energy and low cost, it has greatly advanced With the development of bioinformatics, many genomes are studied based on this platform. However, due to the limitation of read length, and complex genomes contain many high GC and highly repetitive regions, Illumina's performance in the assembly of these genomes is not ideal. [0003] PacBio RSII is currently the most mature third-generation sequencing platform on the market. Its average sequencing read length ranges from 2k at the beginning to 14k at present, and can span most of the repeating regions. It has great ad...

AI Technical Summary

Problems solved by technology

[0004] However, due to the relatively high error rate of single-molecule sequencing, the error rate of single sequencing is 15%, and the error rate of cycle sequencing is about 8%. There is a big gap between its accuracy and second-generation sequencing technology. It is very computationally resource-intensive, and the calculation of large genomes is so huge that only a few institutions can afford to use this technology

Images