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Next-generation sequencing technologies have greatly promoted the genomic study of prokaryotes.However,highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology.Reference-assisted tools are promising in genome assembly,but tend to result in false assembly when the assigned reference has extensive rearrangements.Herein,we present GAAP,a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Frameworks(cGOFs)described in our previous study.