YuliaNuzhnenko Agent Skill: CARD & ResFinder Antimicrobial Resistance Skill
📌 Description
Scans bacterial genome assemblies against CARD (Comprehensive Antibiotic Resistance Database) and ResFinder to map drug-class resistance heatmaps.
🤖 Agent Execution Protocol
When an AI Agent is tasked with card-amr-profiler:
- Input Validation: Verify that the required input files or coordinates are supplied.
- Environment Check: Ensure dependencies (
RGI (Resistance Gene Identifier), ResFinder, Seaborn) are installed. - Execution: Run the protocol pipeline snippet below.
- Output Generation: Produce actionable Markdown/JSON summaries with publication figures.
💻 Protocol Code Snippet
rgi main --input_sequence genome.fasta --output_file amr_results --input_type contig --local
📥 Input & Output Specifications
Input Contract
- Target Files: Valid input data matching domain formats.
- Parameters: Quality thresholds and cutoffs.
Output Contract
- Results Table: Structured summary dataframe or matrix.
- Visualization: Rendered SVG/PNG figures.
📄 License
Distributed under the MIT License. See LICENSE for details.