Third-generation PacBio sequencing data comparison method

A technology for sequencing data and comparison, applied in the field of biological information, can solve problems affecting biological analysis, etc., and achieve the effect of saving comparison time, saving memory and comparison time, and improving accuracy and speed.

Active Publication Date: 2016-10-12
HANGZHOU HEYI GENE TECH
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Problems solved by technology

And these comparison software will compare and output these repeated sequences, thus affecting the subsequent biological analysis (such as assembly, expression analysis, etc.)

Method used

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  • Third-generation PacBio sequencing data comparison method
  • Third-generation PacBio sequencing data comparison method
  • Third-generation PacBio sequencing data comparison method

Examples

Experimental program
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Embodiment

[0032] (1) Use the second-generation Illumina sequencing data to build a kmer model and extract unique-kmer from it

[0033] Use jellyfish software to perform k-mer statistics on the second-generation Illumina sequencing data, and break all the data into fragments of length k (called k-mer). The abscissa is the frequency of the k-mer, and the ordinate is the frequency. Types of k-mers. According to the k-mer distribution diagram, the k-mer within twice the main peak is obtained as the unique-kmer. For k≤17, a bit file (*.bit) with a size of 2G is used to store it. For the case of k>17, the The unique-kmer is stored in the (*.h5) file in the GATB open source package. Wherein, the second-generation Illumina sequencing data refers to the next-generation sequencing data obtained through a sequencer of Illumina Company.

[0034] According to the above method, write the following program to extract unique-kmer. The specific operation commands are as follows:

[0035]

[0036] ...

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Abstract

The invention provides a third-generation PacBio sequencing data comparison method capable of effectively reducing comparison errors caused by repeated sequences. According to the method, a k-mer model is established by using second-generation Illumina data; unique-kmer is extracted; and in third-generation PacBio sequencing data comparison, unique-kmer is used as a seed used in the comparison, so that the influence of the repeated sequences can be greatly reduced and the comparison speed can be increased.

Description

technical field [0001] The present invention relates to the technical field of biological information, in particular to a method for comparing DNA sequences, which uses the second-generation Illumina sequencing data to model and extract key information, and uses the key information to assist the comparison of the third-generation PacBio sequencing data. Background technique [0002] For the sequencing data of the third generation of PacBio, the error rate of a single sequencing is about 15%. There are not many alignment software that specifically support the third generation. At present, the following two software are most used: (1) blasr; (2) dalign. [0003] These two are very good three-generation comparison software, which can support PacBio's high error rate. Due to the presence of repetitive sequences in the genome itself, they have highly similar sequences. These comparison software will compare and output these repeated sequences, thereby affecting subsequent biolog...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/20
CPCG16B25/00
Inventor 詹东亮王军一郝美荣何荣军俞凯成高金龙蔡庆乐
Owner HANGZHOU HEYI GENE TECH
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