Abstract
Next generation sequencing technology has allowed efficient production of draft genomes for many organisms of interest. However, most draft genomes are just collections of independent contigs, whose relative positions and orientations along the genome being sequenced are unknown. Currently, several tools, including CAR that was designed by our laboratory in 2014, have been developed to order and ori-ent the contigs of draft genomes using single reference genomes. In fact, all these single-reference based tools may produce erroneous scaffolds of draft genomes, if the evolutionary relationship between the draft and reference genomes is not close-ly related. In other words, it may not be sufficient to use single reference genomes for producing correct scaffolds of draft genomes. Recently, there is a tool called Ragout that can utilize multiple reference genomes to generate more accurate scaf-folds of draft genomes. However, Ragout requires users to input a phylogenetic tree of the draft and reference genomes, which actually cannot be easily obtained by us-ers in advance. In this study, motivated by Ragout, we try to improve our single reference-based tool CAR by developing two multiple reference-based tools, called multi-CAR and Ragout-CAR, that can utilize multiple reference genomes to pro-duce high-quality scaffolds of draft genomes. Basically, multi-CAR is designed based on only CAR and does not require users to input a phylogenetic tree, and Ra-gout-CAR is designed based on both Ragout and CAR and can automatically create a phylogenetic tree. Finally, our experimental results on several testing datasets have shown that in most cases, multiple reference-based tools have better perfor-mance than their single reference-based tools. In addition, there are some testing cases showing that Ragout-CAR is better than Multi-CAR, while there are some other testing cases showing that Multi-CAR is better than Ragout-CAR. All these results demonstrate that both Multi-CAR and Ragout-CAR can be useful for pro-ducing high-quality scaffolds of draft genomes using multiple reference genomes.