doi: 10.4304/jsw.9.8.2160-2168
De Bruijn Graph based De novo Genome Assembly
- Computer Science and Engineering, Chittagong University of Engineering and Technology Chittagong, Bangladesh
Abstract
The Next Generation Sequencing (NGS) is an important process which assures inexpensive organization of vast size of raw sequence data set over any traditional sequencing systems or methods. Various aspects of NGS like template preparation, sequencing imaging and genome alignment and assembly outlines the genome sequencing and alignment .Consequently, deBruijn Graph (dBG) is an important mathematical tool that graphically analyzes how the orientations are constructed in groups of nucleotides. Basically, de Bruijn graph describe the formation of the genome segments in a circular iterative fashions. Some pivotal de Bruijn graph based de novo algorithms and software package like T-IDBA, Oases, IDBA-tran, Euler, Velvet, ABySS, AllPaths, SOAPdenovo and SOAPdenovo2 have illustrated here.
Keywords
- Next Generation Sequencing (NGS)
- deBrui
How to Cite
Mohammad Ibrahim Khan and Md. Sarwar Kamal, "De Bruijn Graph based De novo Genome Assembly," Journal of Software, vol. 9, no. 8, pp. 2160-2168, 2014. https://doi.org/ 10.4304/jsw.9.8.2160-2168
Copyright & License
Copyright © 2014 by the authors. This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).