Abstract: The present invention is a computerized system for managing the finishing of a complete genome, or fragment thereof or a related derivative thereof, having a PrimerEngine component operative to identify combinations of primers and templates according to suitability for gap closure, quality enhancement or coverage; a Project Manager component operative to identify projects, users, and sequencing data sources; an Assembly module operative by reassembling nucleic acid sequences into artificial chromosomes or genomes; a Data Visualization Module operative to provide information about reads, and contigs; a Report module operative to provide information about a project; an Order module operative to provide information about the status of an order or sequence-reaction; and a Project Administration component operative to create projects and to assign user access to the projects, methods of use thereof.