{"paper_id":"0511b967-e8e8-4c5f-b009-d943701d5f43","body_text":"Full text loading...\nAbstract\nAccurate 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.\n- Received:\n- Version Posted:\nFunding\n-\nAustralian Research Council\n(Award DE250100677)\n- Principal Award Recipient: Ryan R Wick\n-\nAustralian Research Council\n(Award DP240102465)\n- Principal Award Recipient: Timothy P Stinear\n-\nNational Health and Medical Research Council\n(Award APP1105525)\n- Principal Award Recipient: Timothy P Stinear","source_license":"CC-BY-4.0","license_restricted":false}