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

Abstract

Recent developments in sequencing technologies have given the opportunity to sequence many bacterial genomes with limited cost and labor, compared to previous techniques. However, a limiting step of genome sequencing is the finishing process, needed to infer the relative position of each contig and close sequencing gaps. An additional degree of complexity is given by bacterial species harboring more than one replicon, which are not contemplated by the currently available programs. The availability of a large number of bacterial genomes allows geneticists to use complete genomes (possibly from the same species) as templates for contigs mapping.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.

Figure 1

CONTIGuator. a) Program flowchart: the input contigs are mapped to the reference using the combination of Blast and MUMmer, generating a map (viewable with ACT), Primer3 provides a series of PCR primers that can be used to generate a new set of contigs, from which the process can be iterated again; b-c-d-e) ACT visualization: the reference genome is on top, pseudocontig on bottom; b) a putative primer placement over two near contigs; c) a section of no synteny in an otherwise fully syntenic contig; d) a region of the reference genome with no homolog in the mapped contig; e) the same region in d) highlighted, since it harbors a tblastn hit against the excluded contigs; f-g) verification of structural clues in ACT: the closed genome of Sinorhizobium meliloti BL225C is on top, the reference genome in the middle and the contigs on bottom.