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Method of carrying out scaffolding based on long fragments

A long-fragment and skeleton technology, which is applied in the field of skeleton assembly based on long fragments, can solve problems such as high cost, increased library construction and sequencing, and long experimental cycle, achieving fast running speed, improved connection accuracy, and high application range Effect

Active Publication Date: 2017-10-20
WUHAN FRASERGEN CO LTD
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Problems solved by technology

The biggest inconvenience is that in order to obtain mate pair / pair-end sequences, it is necessary to increase the amount of library construction and sequencing from the experimental level. The experimental cycle is long and expensive.

Method used

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  • Method of carrying out scaffolding based on long fragments
  • Method of carrying out scaffolding based on long fragments
  • Method of carrying out scaffolding based on long fragments

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Embodiment Construction

[0031] The principles and features of the present invention are described below in conjunction with examples, which are only used to explain the present invention and are not intended to limit the scope of the present invention.

[0032] The above method is compiled into a software program to run, and the genome skeleton assembly of Saccharomyces cerevisiae is taken as an example to demonstrate. Saccharomyces cerevisiae is one of the most classic model organisms. In eukaryotes, its status is equivalent to Escherichia coli in prokaryotic model organisms. The analysis of yeast gene sequence can provide basis for many molecular biological mechanisms of eukaryotes, therefore, obtaining accurate, complete and continuous yeast genome has important scientific value.

[0033] The three-generation sequencing of the Saccharomyces cerevisiae genome was performed to obtain 526Mb original read sequences, which were used to assemble 28 splicing blocks and perform skeleton assembly to explai...

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Abstract

The invention relates to a method of carrying out scaffolding based on long fragments. The method is characterized by including the following steps: S1, obtaining long-fragment sequence data and a genome splicing result, and obtaining an estimated genome size, a genome splicing size and a contig number; S2, evaluating an insert length range between a mate pair according to the long-fragment sequence data and the genome splicing result; S3, generating a mate pair library according to the long-fragment sequence data and the insert length range; and S4, using the mate pair library, which is obtained in the S3, to carry out scaffolding on the genome splicing result to obtain a scaffolding result. Through using the method of the invention, an existing long-fragment sequence can be directly utilized to obtain the mate pair library in a case where additional mate pair or pair end sequencing is not needed, and thus next scaffolding is completed.

Description

technical field [0001] The present invention relates to the field of genome sequencing, more particularly, to a method for backbone assembly based on long fragments. Background technique [0002] Since the off-machine results of high-throughput sequencing are not a complete and continuous genome, but a series of overlapping fragments, specific assembly algorithms and software must be used to assemble these fragments into a relatively complete genome. However, due to insufficient raw data or defects in assembly software, ideal assembly results are often not obtained, especially in complex regions of the genome, which are generally difficult to assemble, thus leaving some regions of unknown length and sequence in the final result, and, Due to the presence of such regions, the sequence of the assembled fragments cannot be determined. In order to determine the order, another technique has been developed: the scaffolding technique. This technology can obtain the sequences of tw...

Claims

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Application Information

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IPC IPC(8): G06F19/22
CPCG16B30/00
Inventor 邬三毛郭文浒肖世俊陈楠生
Owner WUHAN FRASERGEN CO LTD
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