Multi-CAR: a tool of contig scaffolding using multiple references.
BACKGROUND
A draft genome assembled by current next-generation sequencing techniques from short reads is just a collection of contigs, whose relative positions and orientations along the genome being sequenced are unknown. To further obtain its complete sequence, a contig scaffolding process is usually applied to order and orient the contigs in the draft genome. Although several single reference-based scaffolding tools have been proposed, they may produce erroneous scaffolds if there are rearrangements between the target and reference genomes or their phylogenetic relationship is distant. This may suggest that a single reference genome may not be sufficient to produce correct scaffolds of a draft genome.


RESULTS
In this study, we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new one called Multi-CAR such that it can utilize multiple complete genomes of related organisms as references to more accurately order and orient the contigs of a draft genome. In practical usage, our Multi-CAR does not require prior knowledge concerning phylogenetic relationships among the draft and reference genomes and libraries of paired-end reads. To validate Multi-CAR, we have tested it on a real dataset composed of several prokaryotic genomes and also compared its accuracy performance with other multiple reference-based scaffolding tools Ragout and MeDuSa. Our experimental results have finally shown that Multi-CAR indeed outperforms Ragout and MeDuSa in terms of sensitivity, precision, genome coverage, scaffold number and scaffold N50 size.


CONCLUSIONS
Multi-CAR serves as an efficient tool that can more accurately order and orient the contigs of a draft genome based on multiple reference genomes. The web server of Multi-CAR is freely available at http://genome.cs.nthu.edu.tw/Multi-CAR/ .
Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
Kun-Tze
KT
Chen
Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
Cheih-Jung
CJ
Chen
Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
Hsin-Ting
HT
Shen
Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
Chia-Liang
CL
Liu
Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
Shang-Hao
SH
Huang
Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan. cllu@cs.nthu.edu.tw.
Chin Lung
CL
Lu
D001419:Bacteria / Q000235:genetics; D020451:Contig Mapping / Q000379:methods*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
Bioinformatics; Contigs; Multiple references; Next-generation sequencing; Scaffolding