Read and distance distribution based genome De novo sequence splicing method

Abstract

The invention discloses a read and distance distribution based genome De novo sequence splicing method. In the method, overlap relation between reads is stored by means of a De Bruijn diagram, and a new scoring function is provided on the basis of read distribution to apply to processes of contig construction, scaffolding and blank area filling and the like. The scoring function takes full consideration of sequencing depth, k-mer frequency and deviation of insertsize of a complex repeated region. The method is simple and easy to implement, and has good splicing effect in terms of different simulated and real sequencing data, and has high continuity and integrity as compared with the other sequence splicing method.

Description

technical field [0001] The invention relates to the field of bioinformatics, in particular to a genome de novo sequence splicing method based on read counts and distance distribution. Background technique [0002] Genome generally refers to all coding and non-coding deoxyribonucleic acid (DNA) sequences. DNA sequence is the carrier of genetic information and the basis for the synthesis of protein amino acid sequence, and guides the development of organisms and the operation of life functions. Therefore, DNA sequence is the decisive factor for the existence and development of life, and everything that happens in life activities is inextricably linked with DNA sequence. DNA sequences have become indispensable knowledge in basic biological research and in numerous applied fields such as diagnostics, biotechnology, forensic biology, and biosystematics. Genome sequencing refers to the analysis of the base sequence of a specific DNA fragment, that is, the arrangement of adenine ...

AI Technical Summary

Problems solved by technology

However, this method does not consider the sequencing depth when designing the scoring function

[0008] At present, although existing methods use paired-end reads for sequence assembly, there are still two problems that need to be further resolved: (1) Existing methods can eliminate a part of repetitive regions by using partial read sets generated by paired-end reads coming, but cannot overcome the influence of some complex repeat regions

(2) Existing methods often assume that the sequencing depth is balanced, but in fact the sequencing depth is often unbalanced

Although the IDBA-UD method raises the problem of sequencing depth, this method only judges the correctness of the node itself and deletes the wrong node from the k-mer frequency ratio between adjacent nodes, without contig expansion, scaffolding and Consider the sequencing depth in the three steps of filling the gap

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