Genome assembly method for constructing overlength continuous DNA (DeoxyriboNucleic Acid) sequence

Abstract

The invention discloses a genome assembly method for constructing an overlength continuous DNA (DeoxyriboNucleic Acid) sequence. The genome assembly method comprises the following steps: S1, finding out an overlapping region between each pair of known DNA sequences; S2, starting from a free tail end of any anchoring sequence fragment, extending the anchoring sequence fragment by using a Read sequence overlapped with the anchoring sequence fragment, cycling for multiple times until the Read sequence which can match the tail end of the other anchoring sequence fragment is encountered and obtaining one or more path sequences; S3, selecting at most one sequence from all the path sequences as an effective linker sequence for linking the tail end of a starting anchoring sequence fragment to thetail end of another endpoint anchoring sequence fragment; S4, linking the starting anchoring sequence fragment with the corresponding endpoint anchoring sequence fragment by utilizing the effective linker sequence; taking the effective linker sequence as a new anchoring sequence fragment after linking or recording the free tail end of the remaining anchoring sequence fragment and switching to S2;repeating S2 to S4 and finally, forming the overlength continuous DNA sequence. The genome assembly method disclosed by the invention has the advantage that the sequences of the whole chromosome and the whole genome are more favorably restored.

Description

technical field [0001] The invention relates to a genome assembly method for constructing superlong continuous DNA sequences, and belongs to the technical field of genome assembly. Background technique [0002] The sequencer generates random reads (Reads) by sequencing the genome fragments. The distribution of these reads on 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 fragments (Contig), and finally restore the sequence of the entire chromosome and the entire genome. This assembly process generally includes three steps: assembly of continuous fragments (Contig), assembly of discontinuous fragments with gaps (Scaffold), and gap filling (GF). The difficulty of genome assembly comes from the existence of a large number of repetitive sequences in the genome (that is, two / segments or multiple / sequences with similar or identical sequences). Repeats in the genome can be di...

AI Technical Summary

Problems solved by technology

Due to the tolerance of errors in sequence comparison, the Reads from different copies of the repeat sequence will be compressed together, and the repeat sequences of different copies will become one, so they cannot be distinguished

However, due to the existence of intersection nodes, the formed repetitive sequence Contig is disconnected at the compressed start and end positions, resulting in the fragmentation of the assembled Contig, which in turn makes it impossible to truly restore the entire original genome sequence

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