Nucleotide sequence assembly method and device

Abstract

The invention discloses a nucleotide sequence assembly method and device. The method comprises the steps of receiving sequencing sequences, wherein the sequencing sequences comprise reads and sequenced data; creating an original assembly graph according to the reads; aligning the sequenced data to the edges of the original assembly graph; selecting anchor point edges from an edge set of the original assembly graph; creating partial subgraphs with the anchor point edges as the centers; simplifying the partial subgraphs, repeatedly selecting the anchor point edges from a simplification result, and carrying out processing till no new anchor point edge exists; after processing, combining the left local subgraphs, and outputting a combination result as an assembly result. According to the method of the invention, sequenced data is aligned to the original assembly graph composed of the reads, the anchor point edges are selected from the original assembly graph and the partial subgraphs are built according to the anchor point edges, and then through simplification and combination of the partial subgraphs, a longer path is obtained, so that the problem of path selection of repetitive sequences between the anchor point edges is solved, the assembly of the sequencing sequences is completed, and the scaffold creation effect is likely to be improved.

Description

technical field [0001] The invention relates to the field of biological information processing, in particular to a nucleic acid sequence splicing method and device. Background technique [0002] In the development of genome sequencing technology, the second-generation sequencing technology with low cost, high sequencing throughput (also known as high throughput, refers to the amount of data output obtained within a certain period of time), and more accurate features has brought unprecedented application prospects , such as genome assembly, structural variation detection, etc. The reads (reads, small fragments obtained by random scrambling of DNA sequences) obtained by the second-generation sequencing technology are not only short in length, but also extremely large in number and high in coverage, which brings unprecedented difficulties to sequence assembly. Genome sequencing A key step in is sequence assembly. Sequence splicing is to compare and merge small reads into larg...

AI Technical Summary

Problems solved by technology

[0003] The basic splicing problem faced by the second-generation sequencing technology is that due to the short read length of the second-generation sequencing technology, it brings difficulties to the splicing algorithm, including how to deal with sequencing errors and how to deal with repeated sequences

In real genome projects, the repeat sequence content of large genomes, especially plant genomes, is very high, and some repeat sequences are as high as 60%. The short and fragmented contig (contig) sequence will affect the construction of scaffold (scaffold, which is composed of sequence-determined contigs connections) and hole filling in the subsequent splicing process, and the effect is not good.

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