@article{(Open Science Index):https://publications.waset.org/pdf/2920,
	  title     = {SIMGraph: Simplifying Contig Graph to Improve de Novo Genome Assembly Using Next-generation Sequencing Data},
	  author    = {Chien-Ju Li and  Chun-Hui Yu and  Chi-Chuan Hwang and  Tsunglin Liu  and  Darby Tien-Hao Chang},
	  country	= {},
	  institution	= {},
	  abstract     = {De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.
},
	    journal   = {International Journal of Biotechnology and Bioengineering},
	  volume    = {6},
	  number    = {7},
	  year      = {2012},
	  pages     = {445 - 450},
	  ee        = {https://publications.waset.org/pdf/2920},
	  url   	= {https://publications.waset.org/vol/67},
	  bibsource = {https://publications.waset.org/},
	  issn  	= {eISSN: 1307-6892},
	  publisher = {World Academy of Science, Engineering and Technology},
	  index 	= {Open Science Index 67, 2012},
	}