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

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.