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The Next Generation Sequencing Data Processing

Author: ZhangJun
Tutor: YuanBo
School: Shanghai Jiaotong University
Course: Computer Software and Theory
Keywords: Next-Generation Sequencing Image processing Image registration Base recognition Image analysis Signal processing
CLC: TP391.41
Type: Master's thesis
Year: 2011
Downloads: 62
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Abstract

With the development of the next-generation gene sequencing technology (NGS, Next Generation Sequencing), laboratory equipment and process matures, more and more companies launched their own sequencing platforms, gene sequencing has been moving away from the gene laboratory, so More research group and researchers are beginning to enter the field. With it comes, NGS data processing is facing increasing demands and challenges, researchers can not meet the basic data processing procedures provided in the use of gene sequencing machine vendors, and switch to a more open, flexible first Tripartite processing software. In this paper, we re-examine the process of NGS genomic data processing from the original image data processing to the base to identify the complete set of the NGS genetic sequencing data processing algorithms. Wherein, in some of the existing NGS data processing tool, the image processing section is generally used in the level set segmentation method or a simple use of the Laplacian for processing. After careful analysis of these results, we found that they in fact can not be precise complete the task of positioning and identification of the gene cluster, we redesigned the processing algorithms (NRDPT NGS Raw Data Processing Tool). Unlike existing several processing method, the method using the gene cluster positioning algorithm based on the edge and Hough transform, and effectively improve the positioning accuracy. And, on the basis of accurate gene cluster, we have designed a two-step registration strategy greatly improves the efficiency (~ 9-fold increase in the traditional algorithm). In this article, we will discuss in detail this part of the algorithm. In nucleotide recognition section now Some studies are based on the Illumina sequencing platform sequencing data, these studies mainly used to try to fix the instrument often occur phase Mansian of these problems are generally derived biochemical The defects of the reaction. The new sequencing methods (such as SoLiD, HYK, etc.), because the update of the sequencing process, these problems do not exist. In this article, we discuss the problems that would arise in the different sequencing methods for base recognition process, carefully consider several different base recognition strategy, we completed the sequencing process based on the ligation reaction the base recognition methods, and get a good result. Gene sequencing technology has developed rapidly, the course of our research based on our completely independent intellectual property rights, Inconel the P-STARII gene sequencing machines to start machines and sequencing processes are constantly upgraded in the entire research process, these The uncertainty often increase the difficulty of our study, but it also illustrates the field is rapidly developing. Here, we look forward to NGS sequencing technology really mature, and eventually into the clinical field.

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