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Volume 10, Issue 5

Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing Open Access

Abstract

Whole-genome reconstruction of bacterial pathogens has become an important tool for tracking transmission and antimicrobial resistance gene spread, but highly accurate and complete assemblies have largely only historically been achievable using hybrid long- and short-read sequencing. We previously found the Oxford Nanopore Technologies (ONT) R10.4/kit12 flowcell/chemistry produced improved assemblies over the R9.4.1/kit10 combination, however long-read only assemblies contained more errors compared to Illumina-ONT hybrid assemblies. ONT have since released an R10.4.1/kit14 flowcell/chemistry upgrade and recommended the use of Bovine Serum Albumin (BSA) during library preparation, both of which reportedly increase accuracy and yield. They have also released updated basecallers trained using native bacterial DNA containing methylation sites intended to fix systematic basecalling errors, including common adenosine (A) to guanine (G) and cytosine (C) to thymine (T) substitutions. To evaluate these improvements, we successfully sequenced four bacterial reference strains, namely , , and , and nine genetically diverse bloodstream infection-associated isolates from different phylogroups and sequence types, both with and without BSA. These sequences were assembled and compared against Illumina-corrected reference genomes. In this small evaluation of 13 isolates we found that nanopore long-read-only R10.4.1/kit 14 assemblies with updated basecallers trained using bacterial methylated DNA produce accurate assemblies with ≥40×depth, sufficient to be cost-effective compared with hybrid ONT/Illumina sequencing in our setting.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genome sequencing , hybrid assembly and long-read assembly
Funding
This study was supported by the:
  • Wellcome Trust (Award 203141/Z/16/Z)
    • Principle Award Recipient: NicoleStoesser
  • NIHR Oxford Biomedical Research Centre (Award NIHR200915)
    • Principle Award Recipient: NicoleStoesser
© 2024 Not applicable
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing
M Gen 10, 001246 (2024); https://doi.org/10.1099/mgen.0.001246
/content/journal/mgen/10.1099/mgen.0.001246
/content/journal/mgen/10.1099/mgen.0.001246
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