r2cat: synteny plots and comparative assembly

Abstract

Recent parallel pyrosequencing methods and the increasing number of finished genomes encourage the sequencing and investigation of closely related strains. Although the sequencing itself becomes easier and cheaper with each machine generation, the finishing of the genomes remains difficult. Instead of the desired whole genomic sequence, a set of contigs is the result of the assembly. In this applications note, we present the tool r2cat (related reference contig arrangement tool) that helps in the task of comparative assembly and also provides an interactive visualization for synteny inspection.

Fig. 1.

Synteny plots produced by r2cat. The contigs of C.urealyticum (NCBI number: NC_010545) are mapped onto the reference sequence of C.jeikeium (NC_007164).