ingap-sf

inGAP-sf is an effective scaffolder to generate high-quality and continuous scaffolds. inGAP-sf achieves this by using a new strategy based on the combination of Dlink and Plink graphs, in which Dlink is used to increase graph connectivity and to decrease graph complexity and Plink is employed to supervise the traversing process on the Dlink graph. Such advantage greatly facilitates the assembly of short-repeat enriched regions. Moreover, a new comprehensive decision model is developed to eliminate the noise routes accompanying with the introduced Dlink. Through extensive evaluations on both simulated and real datasets, we demonstrated that inGAP-sf outperforms most of the genome scaffolding algorithms by generating more accurate and continuous assembly, especially for short repetitive regions.