ContigScape: a Cytoscape plugin facilitating microbial genome gap closing

Biao Tang, Qi Wang, Minjun Yang, Feng Xie, Yongqiang Zhu, Ying Zhuo, Shengyue Wang, Hong Gao, Xiaoming Ding, Lixin Zhang, Guoping Zhao, Huajun Zheng

    Research output: Contribution to journalArticle

    Abstract

    BACKGROUND: 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.

    RESULTS: 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.

    CONCLUSIONS: 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.

    Original languageEnglish
    Pages (from-to)289
    JournalBMC Genomics
    Volume14
    DOIs
    Publication statusPublished - 30 Apr 2013

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  • Cite this

    Tang, B., Wang, Q., Yang, M., Xie, F., Zhu, Y., Zhuo, Y., Wang, S., Gao, H., Ding, X., Zhang, L., Zhao, G., & Zheng, H. (2013). ContigScape: a Cytoscape plugin facilitating microbial genome gap closing. BMC Genomics, 14, 289. https://doi.org/10.1186/1471-2164-14-289