AlignGraph

AlignGraph is a software tool designed to improve the assembly of genomes by extending and joining de novo-assembled contigs or scaffolds with the aid of closely related reference genomes. It aligns paired-end reads and preassembled contigs or scaffolds to a close reference genome, and builds a novel data structure called the PE multipositional de Bruijn graph to extend the initial assemblies while avoiding incorrect extensions and early terminations. AlignGraph can substantially improve the contigs and scaffolds from several assemblers, as demonstrated by its ability to increase the N50 of the extendable contigs of Arabidopsis thaliana and human by 89.9-94.5% and 80.3-165.8%, respectively