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Related Experiment Video

Updated: Feb 18, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Completing bacterial genome assemblies with multiplex MinION sequencing.

Ryan R Wick1, Louise M Judd1, Claire L Gorrie1

  • 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville Victoria 3010, Australia.

Microbial Genomics
|November 28, 2017
PubMed
Summary
This summary is machine-generated.

Oxford Nanopore Technologies (ONT) sequencing combined with Illumina data provides fully resolved bacterial genomes. This hybrid approach is valuable for tracking mobile genetic elements and antimicrobial resistance determinants in bacteria.

Keywords:
Klebsiella pneumoniaegenome assemblyhybrid assemblylong-read sequencingmultiplex sequencingoxford nanopore

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Illumina sequencing is widely used for bacterial whole genomes but short reads limit genomic structure resolution.
  • Resolving mobile genetic elements, including antimicrobial resistance determinants, requires long-read sequencing.
  • Oxford Nanopore Technologies (ONT) platforms offer long-read sequencing capabilities.

Purpose of the Study:

  • To evaluate the effectiveness of ONT MinION sequencing for bacterial genome finishing.
  • To compare hybrid assembly (ONT + Illumina) with ONT-only assembly for bacterial genomes.
  • To demonstrate the utility of multiplexed ONT sequencing for high-throughput applications.

Main Methods:

  • Sequencing of 12 *Klebsiella pneumoniae* isolates using ONT MinION on a single flow cell.
  • Hybrid genome assembly using a combination of ONT and Illumina reads with Unicycler.
  • ONT-only genome assembly using Canu, followed by Nanopolish error correction.

Main Results:

  • Fully resolved bacterial genome assemblies were achieved with minimal manual intervention using the hybrid approach.
  • ONT-only assembly with Canu resulted in fewer resolved genomes and higher error rates.
  • Multiplexed ONT sequencing proved effective for high-throughput bacterial genome finishing.

Conclusions:

  • Hybrid assembly using ONT and Illumina reads is a powerful strategy for complete bacterial genome resolution.
  • ONT sequencing is a valuable tool for bacterial genome finishing, especially when combined with initial Illumina data.
  • This approach facilitates the study of mobile genetic elements and antimicrobial resistance in bacterial populations.