ContigScape: a Cytoscape plugin facilitating microbial genome gap closing

BMC Genomics

Software

Hong Gao¹  Ying Zhuo¹  Feng Xie¹  Lixin Zhang¹  Qi Wang²  Yongqiang Zhu³  Huajun Zheng³  Minjun Yang³  Shengyue Wang³  Xiaoming Ding⁴  Biao Tang⁵  Guoping Zhao⁶ 

[1] CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100190, Beijing, China;CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100190, Beijing, China;Graduate School of Chinese Academy of Sciences, 100049, Beijing, China;Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, 201203, Shanghai, China;State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, 200433, Shanghai, China;State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, 200433, Shanghai, China;Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, 201203, Shanghai, China;State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, 200433, Shanghai, China;Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, 201203, Shanghai, China;CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China;Department of Microbiology and Li KaShing Institute of Health SciencesThe Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China;

关键词: ContigScape;    Repeat contig;    Microbial;    Visualization;    Linkage;    Gap closing;   

DOI  :  10.1186/1471-2164-14-289

 received in 2012-12-29, accepted in 2013-04-20,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundWith the emergence of next-generation sequencing, the availability of prokaryotic genome sequences is expanding rapidly. A total of 5,276 genomes have been released since 2008, yet only 1,692 genomes were complete. The final phase of microbial genome sequencing, particularly gap closing, is frequently the rate-limiting step either because of complex genomic structures that cause sequence bias even with high genomic coverage, or the presence of repeat sequences that may cause gaps in assembly.ResultsWe have developed a Cytoscape plugin to facilitate gap closing for high-throughput sequencing data from microbial genomes. This plugin is capable of interactively displaying the relationships among genomic contigs derived from various sequencing formats. The sequence contigs of plasmids and special repeats (IS elements, ribosomal RNAs, terminal repeats, etc.) can be displayed as well.ConclusionsDisplaying relationships between contigs using graphs in Cytoscape rather than tables provides a more straightforward visual representation. This will facilitate a faster and more precise determination of the linkages among contigs and greatly improve the efficiency of gap closing.

【 授权许可】

Unknown   
© Tang 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.