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ContigScape: a Cytoscape plugin facilitating microbial genome gap closing

Biao Tang12, Qi Wang36, Minjun Yang2, Feng Xie3, Yongqiang Zhu2, Ying Zhuo3, Shengyue Wang2, Hong Gao3, Xiaoming Ding1, Lixin Zhang3*, Guoping Zhao1245* and Huajun Zheng2*

Author Affiliations

1 State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200433, China

2 Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China

3 CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100190, China

4 CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China

5 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

6 Graduate School of Chinese Academy of Sciences, Beijing, 100049, China

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BMC Genomics 2013, 14:289  doi:10.1186/1471-2164-14-289

Published: 30 April 2013



With 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.


We 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.


Displaying 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.

ContigScape; Repeat contig; Microbial; Visualization; Linkage; Gap closing