Automating the Closure of Staphylococcus aureus Genomes
Despite significant advances in next generation sequencing modalities, an overwhelming number of genomes still exist in the database which are unfinished or lack closure. For Staphylococcus aureus, the Genome Assembly and Annotation report shows that out of 4,223 genome projects, only 65 are currently listed as complete. The remainder exist as scaffolds or contigs. One of the challenges in genome completion is misassemblies due to tandem or interspersed repeat regions. Therefore, in partnership with Lucigen Corporation, we developed the use of NxSeq Mate-Pair (MP) libraries in automating the closure of Staphylococcus aureus genomes. We have tested three different sequencing modalities: Nextera Kits run with Illumina MiSeq sequencing, Pacific Biosciences SMRTbell libraries with PacBio RS sequencing, and Lucigen NxSeq libraries run on Illumina HiSeq sequencers, and contrast the results of each in the completion of an ancestral S. aureus genome, which we term Tager 104.