Abstract
Next generation sequencing technologies have allowed us to efficiently produce draft genomes for many organisms of interest. However, most draft genomes are just col-lections of independent contigs whose relative positions and orientations along the genome being sequenced are unknown. Currently, several scaffolding tools, including CAR that was designed by our laboratory in 2014, have been developed to order and orient the contigs of draft genomes using single complete reference genomes. How-ever, most of these scaffolding tools can apply only on a complete reference genome. This may reduce their usability in practice because in current public databases, the availability of draft genomes greatly exceeds that of completely sequenced ones. In 2015, our laboratory published a near-linear time scaffolding algorithm that can use a draft genome as a reference to order and orient the contigs. In this study, we imple-ment this algorithm into a scaffolding tool named CSAR (Contig Scaffolding using Algebraic Rearrangement Distance) such that it can order and orient the contigs in a target draft genome according to a complete or draft reference genome. In addition, our experimental results have shown that in most cases, our CSAR performs better than other scaffolding tools in terms of sensitivity, precision, F-score and coverage.