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Motivation: Recovering the gene structures is one of the important goals of genome assembly. In low-quality assemblies, and even some high-quality assemblies, certain gene regions are still incomplete; thus, novel scaffolding approaches are required to complete gene regions. Results: We developed an efficient and fast genome scaffolding method called PEP_scaffolder, using proteins to scaffold genomes. The pipeline aims to recover protein-coding gene structures. We tested the method on humandoi:10.1093/bioinformatics/btw378 pmid:27334475 pmcid:PMC5048069 fatcat:woodmztiefewfhw4qgqrbxlhmy