Parallel gene splicing method based on De Bruijn graph

Abstract

The invention relates to the technical field of gene sequencing, and provides a parallel gene splicing method based on a De Bruijn graph. The parallel gene splicing method based on the De Bruijn graph comprises the following steps that S1, the distributed De Bruijn graph is built in parallel; S2, error paths are removed; S3, the De Bruijn graph is simplified on the base of a depth graph traversal method; S4, contig is combined, and scaffold is generated; S5, the scaffold is output. The parallel gene splicing method is based on a trunking system, the De Bruijn graph is built in parallel, and the problems that when large genomes are spliced, as the data volume of the large genomes is too large, graphs cannot be built and further processing cannot be executed in traditional single-machine serial gene splicing algorithms are solved. Meanwhile, in the simplifying process, parallel simplification based on depth graph traversal is carried out, the graph simplifying process is simple, the degree of parallelism is high, and the splicing speed is high.

Description

technical field [0001] The invention relates to the technical field of gene sequencing, in particular to a parallel gene splicing method based on a De Bruijn graph. Background technique [0002] Gene sequencing is one of the most important problems in the field of modern bioinformatics. With the development of modern biology, gene sequencing has been more and more widely used in various fields of society, such as gene diagnosis, gene therapy, drug design and so on. An important step in gene sequencing is gene splicing. [0003] With the widespread application of gene sequencing, on the one hand, it needs to sequence a large number of organisms with large genomes. When sequencing large genomes, the amount of data is very large; on the other hand, this also requires faster and faster gene splicing algorithms. [0004] There are two main types of gene sequence assembly algorithms. The first category is algorithms based on overlap graphs. In the overlap graph, each short se...

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Problems solved by technology

[0008] The present invention provides a parallel gene mosaic method based on De Bruijn graph, aiming at solving the problem that the traditional single machine serial gene mosaic algorithm in the prior art cannot mosaic massive data of large genomes, and the current parallel gene mosaic algorithm cannot quickly Technical issues in genome assembly

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