The gap closure was supported by the related reference contig arrangement tool r2cat, using the complete C. jeikeium K411 genome sequence as a reference [ 21].
The gap closure process was supported by the related reference contig arrangement tool r2cat, using the C. diphtheriae NCTC 13129 genome sequence as a reference [ 13].
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.
Our program r2cat (related reference contig arrangement tool) is able to quickly match a set of contigs onto a related genome, order the contigs according to their matches and display the result in an interactive synteny plot.
The remaining gaps were closed by a PCR strategy that was supported by the related reference contig arrangement tool r2cat [ 13], using the Corynebacterium diphtheriae NCTC 13129 genome sequence as a reference [ 14].
The resulting reads were assembled with the Newbler Assembler software, and the remaining gaps were closed by PCR strategies that were supported by the related reference contig arrangement tool r2cat [ 26] using the genome sequence of C. pseudotuberculosis FRC41 as a reference [ 21].
The subsequent gap closure process was facilitated by in silico predictions of the contig order that were computed by the related reference contig arrangement tool r2cat using the C. pseudotuberculosis FRC41 genome sequence as a reference and the default parameters of the integrated q-gram filter [ 21, 26].
The software treecat (tree based contig arrangement tool) contains a re-implementation of the fast local alignment algorithm swift [ 12], the contig adjacency graph creation, a branch and bound exact TSP algorithm, and the fast layout graph heuristic described in section 'Fast adjacency discovery algorithm'.
Existing automated arrangements tools aimed at early-stage design are capable of generating feasible layouts, but remain a bit of a "black box," lacking methods to elucidate the mechanisms that drive or limit the quality of those layouts.
It shows a simple arrangement of tools on a wall support from four different angles, with the prints butted-up against each other to create an eye-catching abstract arrangement.
