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A genome haploid assembly method and device

An assembly method and haploid technology, applied in the field of genetic engineering, can solve the problems of limited data read length and indistinguishable segment phase relationship, etc., and achieve the effect of improving the degree of precision

Active Publication Date: 2022-03-18
BIOMARKER TECH
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  • Abstract
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  • Application Information

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Problems solved by technology

But again, limited by the data read length, similar to WhatsHap, it only assembles a segment of haploid segments, and the phase relationship between segments is still indistinguishable

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  • A genome haploid assembly method and device
  • A genome haploid assembly method and device

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Embodiment Construction

[0038] In order to make the purpose, technical solutions and advantages of the embodiments of the present invention clearer, the technical solutions in the embodiments of the present invention will be clearly and completely described below in conjunction with the drawings in the embodiments of the present invention. Obviously, the described embodiments It is a part of embodiments of the present invention, but not all embodiments. Based on the embodiments of the present invention, all other embodiments obtained by persons of ordinary skill in the art without creative efforts fall within the protection scope of the present invention.

[0039] figure 1 It is a schematic flow chart of the genome haploid assembly method in the embodiment of the present invention, as figure 1 As shown, a genome haploid assembly method provided in the embodiment of the present invention includes the following steps:

[0040] S101: Obtain SNP information of a reference genome.

[0041] Specifically...

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Abstract

The embodiment of the present invention provides a genome haploid assembly method and device, the method comprising: obtaining the SNP information of the reference genome; respectively using PacBio data and Hi-C data to obtain the phasing information of the SNP information; according to the The phasing information obtains the integrated phasing information of the whole genome; according to the integrated phasing information, the haploid sources of the sequenced fragments of the PacBio data are distinguished, and the genome haploids are assembled respectively. The apparatus performs the method described above. The genome haploid assembly method and device provided in the embodiments of the present invention can distinguish the haploid source of the sequencing fragments of PacBio data by integrating phasing information, and perform genome haploid assembly respectively, so as to realize the haploid assembly of the whole genome , and improve the precision of the assembled genome sequence.

Description

technical field [0001] The embodiments of the present invention relate to the technical field of genetic engineering, and in particular to a genome haploid assembly method and device. Background technique [0002] With the continuous development of sequencing technology, genome assembly technology is also constantly improving. From second-generation sequencing to third-generation sequencing, when the reads of the sequencing fragments are getting longer and longer, the effect of genome assembly is getting better and better. There are currently three genome assembly algorithms, de-bruijn-graph (DBG), overlap-layout-consensus (OLC) and stringgraph, but no matter which method, for the diploid genome, only the haploid size is assembled. A set of genomes without distinction between homologous chromosomes. This situation is mainly limited by the current technical conditions. Due to the high similarity between homologous chromosomes and the length of the reads of the sequencing fr...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/00
Inventor 郑洪坤邓德晶刘敏李绪明黎松刘福刘东源
Owner BIOMARKER TECH