Characteristic kmer based metatypic chromosomal sequence assembly method and application thereof

A technology of sequence assembly and chromosome, applied in the field of bioinformatics

Active Publication Date: 2014-05-21
BGI TECH SOLUTIONS
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0005] In summary, there is currently no effective and simple method for assembling heterotypic chromosome sequences in this field, so there is an urgent need to develop corresponding methods and products

Method used

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  • Characteristic kmer based metatypic chromosomal sequence assembly method and application thereof

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Experimental program
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Embodiment 1

[0106] W heteromorphic sex chromosome assembly in tongue sole semismoothus

[0107] 1. The samples were derived from the blood cells of a female tongue sole and a male tongue sole.

[0108] 2. Use Illumina Hiseq2000 to perform routine whole genome sequencing on the samples.

[0109] Sequencing results: The sequencing data volumes of the father (ZZ) and mother (ZW) are 68GB and 91GB, respectively.

[0110] 3. The first step is to filter the sequencing data and prepare the data profile.

[0111] Sequencing data filtering: sequences with an N content of more than 10%; sequences with a quality value lower than 40; sequences containing primers; sequences with small inserts; sequences with complex PCR;

[0112] The preparation of the data configuration file can be found in the SOAPDenovo instructions.

[0113] The data volumes of the filtered father and mother are 47GB and 64GB, respectively.

[0114] 4. The second step:

[0115] 1) Read in the reads data of two samples, analyz...

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Abstract

The invention relates to a characteristic kmer based metatypic chromosomal sequence assembly method and application thereof. The characteristic kmer based metatypic chromosomal sequence assembly method is characterized by comprising the following steps of: performing whole-genome sequencing for a homoplastic (like XX or ZZ) sample and a metatypic (like XY or ZW) sample; analyzing kmer difference between the two samples based on the data to obtain the characteristic kmer of the metatypic chromosome; and then performing metatypic chromosomal sequence assembly based on the characteristic kmer so as to obtain the complete sequence information of metatypic chromosome. The invention also provides an assembly unit on the basis of the method above.

Description

technical field [0001] The invention belongs to the field of biological information, in particular, the invention relates to a characteristic kmer-based heterotypic chromosome sequence assembly method and its application. Background technique [0002] With the birth of next-generation sequencing technologies 454 (Roche Company), Solexa (Illumina Company) and SOLiD (ABI Company), the sequencing throughput has been rapidly increased, and the cost of sequencing has dropped sharply. This breakthrough has greatly promoted the development of genome science. . [0003] Common sex chromosome classifications are mainly XY type and ZW type. In XY type, XX is female and XY is male (eg human, Drosophila); in ZW type, ZW is female and ZZ is male (eg chicken, tongue sole). Y / W is called a heterotypic sex chromosome. The traditional method of assembling heteromorphic sex chromosomes is whole genome sequencing and assembly, and then selecting the heteromorphic sex chromosome sequences. ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68C12M1/34
CPCC12Q1/6869G16B30/00C12Q2535/122
Inventor 黄铨飞李振宇刘耿刘兵行王俊汪建杨焕明
Owner BGI TECH SOLUTIONS
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