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How benchmarking of bioinformatics tools is essential for informed workflow selection: a case study on SARS-CoV-2
Gabriele Leoni1, Mauro Petrillo2, Man-Hung Eric Tang3
1European Commission, Joint Research Centre (JRC), Ispra, Italy.
Frontiers in Bioinformatics
|May 8, 2026
Summary
Systematic benchmarking is crucial for selecting bioinformatics tools for genomic surveillance. Our study shows that workflow choices significantly impact SARS-CoV-2 subgenomic RNA detection accuracy, emphasizing the need for standardized evaluation.
Area of Science:
- Bioinformatics
- Genomic Surveillance
- Molecular Diagnostics
Background:
- Accurate bioinformatics tool selection is vital for genomic surveillance and biomarker monitoring.
- Effective public health responses to emerging diseases like SARS-CoV-2 depend on reliable data analysis.
Purpose of the Study:
- To demonstrate the importance of systematic benchmarking for selecting optimal bioinformatics workflows.
- To assess the impact of key variables on the detection of SARS-CoV-2 subgenomic RNAs (sgRNAs).
Main Methods:
- Generated 25 synthetic Illumina datasets simulating shotgun and amplicon sequencing.
- Included a real-world wastewater dataset for SARS-CoV-2 sgRNA detection.
- Evaluated the influence of mutation profiles, read lengths, aligner choice, and primer design.
Main Results:
- Observed substantial performance variability among common sgRNA detection tools.
- Shotgun sequencing data analysis was challenging for standard tools and sensitive to mutations.
- Amplicon sequencing enhanced detection sensitivity, but aligner and primer design remained critical factors.
Conclusions:
- Benchmarking bioinformatics workflows is essential to avoid inaccurate conclusions from suboptimal tools.
- Context-aware tool selection and standardized benchmarking practices are necessary for reproducible and reliable bioinformatics analysis.
- This approach supports evidence-based decision-making in public health and policymaking.
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