BenchAMRking

BenchAMRking enables comparison of antimicrobial resistance gene prediction workflows by providing a standardized Galaxy-based platform that illustrates discrepancies in results from different computational approaches applied to microbial whole genome sequencing data.

Key Features:

• Standardized Workflow Comparison: The platform comprises four well-characterised and published workflows that use different computational tools (or tool versions) and interrogate different AMR gene sequence databases.
• Multiple Input Types: The platform focuses on identifying AMR genes from both raw reads and sequence assemblies.
• ISO Certified Workflow Inclusion: One of the four workflows is the ISO certified abritAMR workflow.
• Validated Datasets: The platform was validated using datasets from bacterial species with PCR-verified AMR gene presence or absence information from abritAMR.

Scientific Applications:

• AMR Gene Prediction Benchmarking: Users can investigate potential AMR gene-calling problems associated with their own in silico workflows and protocols by comparing results against standardized workflows.
• Discrepancy Visualization: Users can access, visualise, and explore major discrepancies associated with AMR gene prediction from microbial whole genome sequencing data.
• Semantic Conformity Assessment: The platform addresses the lack of agreement in the naming of AMR genes for results obtained from different prediction workflows.

Methodology:

The platform was developed as a Galaxy-based comparative system and validated using datasets from bacterial species with PCR-verified AMR gene presence or absence information from abritAMR.