The use of Oxford Nanopore native barcoding for complete genome assembly

Gigascience. 2017 Mar 1;6(3):1-6. doi: 10.1093/gigascience/gix001.


Background: The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short read data. The strain we used, MHO_001, represents the important community-acquired methicillin-resistant Staphylococcus aureus lineage USA300.

Findings: Using a hybrid assembly of existing short read and barcoded long read sequences from multiplexed data, we completed a genome of the S. aureus USA300 strain MHO_001. The long read data represented only ∼5% to 10% of an average MinION(TM) run (∼7x genomic coverage), but, using standard tools, this was sufficient to complete the circular chromosome of S. aureus strain MHO_001 (2.86 Mb) and two complete plasmids (27 Kb and 3 Kb). Minor differences were noted when compared to USA300 reference genome, USA300_FPR3757, including the translocation, loss, and gain of mobile genetic elements.

Conclusion: Here we demonstrate that MinION(TM) reads, multiplexed using native barcoding, can be used in combination with short read data to fully complete a bacterial genome. The ability to complete multiple genomes, for which short read data is already available, from a single MinION(TM) run is set to impact our understanding of accessory genome content, plasmid diversity, and genome rearrangements.

Keywords: MinION; Staphylococcus aureus; Whole genome sequencing; bacterial genomics; hybrid assembly; long read; multiplexing; native barcoding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Barcoding, Taxonomic / methods*
  • DNA, Bacterial / genetics
  • Genome, Bacterial / genetics*
  • Genomic Library
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing / methods*
  • Methicillin-Resistant Staphylococcus aureus / classification
  • Methicillin-Resistant Staphylococcus aureus / genetics
  • Nanopores*
  • Reproducibility of Results
  • Species Specificity


  • DNA, Bacterial