ContigScape: a Cytoscape plugin facilitating microbial genome gap closing.

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

SUBMITTER: Tang B 

PROVIDER: S-EPMC3651407 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature