Genome reassembly with high-throughput sequencing data

BMC Genomics

Proceedings

Nathaniel Parrish¹  Eleazar Eskin¹  Benjamin Sudakov² 

[1] Department of Computer Science, University of California Los Angeles, Los Angeles, California, USA;Department of Mathematics, University of California Los Angeles, Los Angeles, California, USA;

关键词: Reference Genome;    Graph Construction;    Reference Marker;    Donor Genome;    Euler Tour;   

DOI  :  10.1186/1471-2164-14-S1-S8

来源: Springer

【 摘 要 】

MotivationRecent studies in genomics have highlighted the significance of structural variation in determining individual variation. Current methods for identifying structural variation, however, are predominantly focused on either assembling whole genomes from scratch, or identifying the relatively small changes between a genome and a reference sequence. While significant progress has been made in recent years on both de novo assembly and resequencing (read mapping) methods, few attempts have been made to bridge the gap between them.ResultsIn this paper, we present a computational method for incorporating a reference sequence into an assembly algorithm. We propose a novel graph construction that builds upon the well-known de Bruijn graph to incorporate the reference, and describe a simple algorithm, based on iterative message passing, which uses this information to significantly improve assembly results. We validate our method by applying it to a series of 5 Mb simulation genomes derived from both mammalian and bacterial references. The results of applying our method to this simulation data are presented along with a discussion of the benefits and drawbacks of this technique.

【 授权许可】

Unknown   
© Parrish et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.