Volume 9 Number 8 (Aug. 2014)
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JSW 2014 Vol.9(8): 2160-2168 ISSN: 1796-217X
doi: 10.4304/jsw.9.8.2160-2168

De Bruijn Graph based De novo Genome Assembly

Mohammad Ibrahim Khan, Md. Sarwar Kamal

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.

Index Terms—Next Generation Sequencing (NGS), deBruijn Graph (dBG), SOAPdenove2


Cite: Mohammad Ibrahim Khan, Md. Sarwar Kamal, "De Bruijn Graph based De novo Genome Assembly," Journal of Software vol. 9, no. 8, pp. 2160-2168, 2014.

General Information

ISSN: 1796-217X (Online)
Frequency:  Quarterly
Editor-in-Chief: Prof. Antanas Verikas
Executive Editor: Ms. Yoyo Y. Zhou
Abstracting/ Indexing: DBLP, EBSCO, CNKIGoogle Scholar, ProQuest, INSPEC(IET), ULRICH's Periodicals Directory, WorldCat, etc
E-mail: jsweditorialoffice@gmail.com
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