Genome assembling method

Abstract

The invention discloses a genome assembling method, comprising the following four steps: sequence comparison, sequence extension, completion of extension and removal of redundancy. Genome-wide assembly is divided into two main steps: assembly of single copy sequence and assembly of remaining sequence, which simplifies the implementation process, makes the whole method fast, efficient and error-free, and greatly improves the continuity of the assembly sequence fragments and the assembly quality. By assembling the whole genome sequence with the method of the invention, the whole genome sequencecan be recovered quickly and efficiently, and the whole chromosome and the whole genome sequence can be recovered more easily. The genome assembling method of the invention can also be used for filling the sequence of the blank region in the genome sequence, in particular, the assembling effect can be greatly improved by combining the genome optical map information or the chromosome grouping sorting information. And for judging whether there is a connection between any two sequences or for estimating a distance between two adjacent sequences.

Description

technical field [0001] The invention relates to a genome assembly method, belonging to the technical field of genome assembly. Background technique [0002] Sequencers generate random read sequence fragments (reads) by sequencing fragments of the genome. The distribution of these reads across the genome is random. The process of genome assembly is to arrange and connect these reads in the correct order, assemble them into base-continuous DNA sequence fragments (continuous fragments), and finally restore the sequence of the entire chromosome and the entire genome. This assembly process generally includes three steps: the assembly of continuous fragments, the assembly of discontinuous fragments with gaps, and the filling of gaps. The difficulty of genome assembly comes from the presence of a large number of repetitive sequences in the genome (that is, two / segments or multiple / sequences of variable length, similar or identical sequences). In addition, the sequencer will make...

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Problems solved by technology

[0004] The purpose of the present invention is to provide a fast and efficient genome assembly method, which can effectively solve the problems existing in the prior art, especially in the prior art by compressing read segments to find paths without intersection nodes in the assembly graph However, due to too many operation steps in this process, the assembly speed is slow and the software complexity is high; also because in the process of compressing similar multi-segment repeat sequences, many reads from different copies of repeat sequences It will be compressed together, causing different copies of the repeated sequence to become one, so they cannot be distinguished; and due to the existence of crossover nodes due to similar sequences or sequencing errors, the formed sequence fragments are disconnected at the compressed start and end positions, resulting in The assembled sequence has the problem of fragmentation of continuous fragments

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