Assembling method for de novo sequencing data based on optics map platform Irys

A technology of sequencing data and assembly method, which is applied in the field of bioinformatics, can solve the problems of information loss and assembly difficulty, and achieve the effect of improving the effect of gene assembly

Active Publication Date: 2016-10-12
GENERGY BIO TECH SHANGHAI CO LTD
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Problems solved by technology

At present, the most commonly used method is NextGeneration Sequencing (NGS), but the NGS method will lose information on a l

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  • Assembling method for de novo sequencing data based on optics map platform Irys
  • Assembling method for de novo sequencing data based on optics map platform Irys
  • Assembling method for de novo sequencing data based on optics map platform Irys

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Embodiment Construction

[0062] In order to make the object, technical solution and advantages of the present invention clearer, various embodiments of the present invention will be described in detail below in conjunction with the accompanying drawings. However, those of ordinary skill in the art can understand that, in each implementation manner of the present invention, many technical details are provided for readers to better understand the present application. However, even without these technical details and various changes and modifications based on the following implementation modes, the technical solution claimed in each claim of the present application can be realized.

[0063] First introduce several concepts used in the present invention:

[0064] 1.read: During the sequencing process, a DNA molecule is first cloned to form several copies, and then these copies are broken into several short fragments that can be directly sequenced. Each fragment is called a "read", and the sequencer genera...

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Abstract

The invention relates to an assembling method for de novo sequencing data based on an optics map platform Irys. The method comprises: using the optics map platform Irys to obtain a gene assembly file; getting a scaffold file: fai file of NGS; preprocessing data: through setting a threshold value, filtering a comparison result whose confidence level is low, combining cmap files, sorting, calculating N50; counting assembling effects: counting comparison results of BioNano and NGS, including the contig of the BioNano, and the length, number, and total quantity of scaffold of NGS; according to the contig of the BioNano and network topological relations among the scaffold of the NGS, analyzing length of the assembled new contig and length of scaffold in a classified manner. The method can assist genome assembly, and obviously improves gene assembly effects of species.

Description

technical field [0001] The present invention relates to bioinformatics, and in particular mainly to assisting de novo sequencing data assembly and detection of structural variation. Background technique [0002] Genome de novo sequencing is genome de novo sequencing, which refers to the sequencing of the whole genome sequence of a species whose genome sequence is unknown or has no genome of a related species. Then, the sequencing sequences were assembled, assembled and annotated by bioinformatics methods to obtain a complete genome sequence map of the species. At present, the most commonly used method is NextGeneration Sequencing (NGS), but the NGS method will cause a large number of repetitive elements and structural variation information to be lost, so it becomes a difficult problem to assemble a complete genome map. [0003] BioNano Genomics has expanded nanochannel technology and developed it into a flexible optical mapping platform Irys with high resolution and extreme...

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Application Information

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IPC IPC(8): G06F19/18
CPCG16B20/00
Inventor 马丰收张艺何飞刘洋
Owner GENERGY BIO TECH SHANGHAI CO LTD
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