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Volume 7, Issue 5

Are reads required? High-precision variant calling from bacterial genome assemblies Open Access

Abstract

Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared to traditional read-based variant-calling methods, using seven closely related isolates sequenced on Illumina and Oxford Nanopore Technologies platforms. By benchmarking multiple assembly and variant-calling pipelines against a ground truth dataset, we found that read-based methods consistently achieved high accuracy. Assembly-based approaches performed well in some cases but were highly dependent on assembly quality, as errors in the assembly led to false-positive variant calls. These findings underscore the need for improved assembly techniques before the potential benefits of assembly-based variant calling (such as reduced computational requirements and simpler data management) can be realized.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genome assembly , microbial genomics , Staphylococcus aureus and variant calling
Funding
This study was supported by the:
  • National Health and Medical Research Council (Award APP1105525)
    • Principal Award Recipient: TimothyP Stinear
  • Australian Research Council (Award DP240102465)
    • Principal Award Recipient: TimothyP Stinear
  • Australian Research Council (Award DE250100677)
    • Principal Award Recipient: RyanR Wick
© 2025 The Authors
  • 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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2025-05-28
2026-04-14

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/content/journal/acmi/10.1099/acmi.0.001025.v3
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Are reads required? High-precision variant calling from bacterial genome assemblies
Access Microbiology 7, 001025.v3 (2025); https://doi.org/10.1099/acmi.0.001025.v3
/content/journal/acmi/10.1099/acmi.0.001025.v3
/content/journal/acmi/10.1099/acmi.0.001025.v3
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