CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

Here we present CONTIGuator, a software tool for contigs mapping over a reference genome which allows the visualization of a map of contigs, underlining loss and/or gain of genetic elements and permitting to finish multipartite genomes. The functionality of CONTIGuator was tested using four genomes, demonstrating its improved performances compared to currently available programs.Our approach appears efficient, with a clear visualization, allowing the user to perform comparative structural genomics analysis on draft genomes. CONTIGuator is a Python script for Linux environments and can be used on normal desktop machines and can be downloaded from http://contiguator.sourceforge.net webcite.In the recent years, the dropping cost of sequencing technologies allowed biologist to easily widen the number of genomic sequences available for the scientific community, especially for bacterial species; moreover, the number of phylogenetically related genomes has also dramatically increased: the number of genera having more than 10 complete genomic sequences is 29 and interestingly, looking at the 12 species with more than 10 genomes fully sequenced, all of them belongs to bacteria (GOLD database [1], November 2010), pointing out the great value of closely related genomes in the so-called bacterial comparative genomics. However, looking at the ongoing or draft genomic projects, within 14 bacterial species with more than 50 running genomic projects, a lack of finishing efforts can be seen, suggesting that the problems encountered while closing a genome (even bacterial ones) are still time-consuming and cannot be easily automated. In fact, to close gaps of draft genomes a series of PCR reactions has to be designed in an iterative fashion.To overcome this problems many programs have been recently developed, using an approach where all the contigs obtained by the first automated assembly run are mapped to a reference closed genome (usually inside the same species or as close as possi