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

2025 · doi:10.1099/acmi.0.001025.v2
preprint OA: closed CC-BY-4.0
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This paper investigates whether accurate nucleotide variant calling in microbial genomics can be achieved from bacterial genome assemblies rather than using traditional read-based methods. Using seven closely related Staphylococcus aureus isolates sequenced with Illumina and Oxford Nanopore platforms, the authors benchmarked multiple assembly/variant-calling pipelines against a ground truth dataset, finding that read-based approaches consistently produced high-accuracy variant calls. Assembly-based variant calling sometimes performed well, but accuracy was highly dependent on assembly quality because assembly errors generated false-positive variants. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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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 Staphylococcus aureus 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 realised.
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Full text loading... 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 Staphylococcus aureus 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 realised. - Received: - Version Posted: Funding - Australian Research Council (Award DE250100677) - Principal Award Recipient: Ryan R Wick - Australian Research Council (Award DP240102465) - Principal Award Recipient: Timothy P Stinear - National Health and Medical Research Council (Award APP1105525) - Principal Award Recipient: Timothy P Stinear

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License: CC-BY-4.0