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Volume 10, Issue 11

Matching excellence: Oxford Nanopore Technologies’ rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content Open Access

Abstract

The reconstruction of complete bacterial genomes is essential for microbial research, offering insights into genetic content, ontology and regulation. While Pacific Biosciences (PacBio) provides high-quality genomes, its cost remains a limitation. Oxford Nanopore Technologies (ONT) offers long reads at a lower cost, yet its error rate raises scepticism. Recent ONT advancements, such as new Flow cells (R10.4.1), chemistry (V14) and duplex mode, improve data quality. Our study compares ONT with PacBio and Illumina, including hybrid data. We used , a bacterium with a genome known for being difficult to reconstruct. By combining data from ONT’s Native Barcoding and a custom-developed BARSEQ method, we achieved high-quality, near-perfect genome assemblies. Our findings demonstrate, for the first time, that the combination of nanopore-only long-native with shorter PCR DNA reads (~3 kb) results in high-quality genome reconstruction, comparable to hybrid data assembly from two sequencing platforms. This endorses ONT as a cost-effective, stand-alone strategy for bacterial genome reconstruction. Additionally, we compared methylated motif detection between PacBio and ONT R10.4.1 data, showing that results comparable to PacBio are achievable using ONT, especially when utilizing the advanced Nanomotif tool.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genome reconstruction , long-read sequencing and single-molecule sequencing
Funding
This study was supported by the:
  • Milk Levy fund (Award CASSANDRA)
    • Principle Award Recipient: LukaszKrych
  • Horizon 2020 Framework Programme (Award H2020-MSCA-IF grant nr. 845658)
    • Principle Award Recipient: PaulinaDeptula
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-11-11
2024-12-09
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Matching excellence: Oxford Nanopore Technologies’ rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content
M Gen 10, 001316 (2024); https://doi.org/10.1099/mgen.0.001316
/content/journal/mgen/10.1099/mgen.0.001316
/content/journal/mgen/10.1099/mgen.0.001316
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