bwa-mem2-dna-aligner
Pass
Audited by Gen Agent Trust Hub on May 11, 2026
Risk Level: SAFEEXTERNAL_DOWNLOADSCOMMAND_EXECUTION
Full Analysis
- [EXTERNAL_DOWNLOADS]: The skill fetches the BWA-MEM2 binary from its official GitHub repository and reference genome data from trusted scientific entities including the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI).
- [COMMAND_EXECUTION]: The skill executes a sequence of bioinformatics command-line tools (
bwa-mem2,samtools,picard,gatk) and inline Python scripts to perform genomic data alignment, sorting, and variant calling. - [PROMPT_INJECTION]: The skill possesses a surface for indirect prompt injection because it processes external genomic data files (FASTQ) that could theoretically contain malicious instructions, though the risk is negligible for this data type.
- Ingestion points: FASTQ files are processed in Step 3 and Step 6 of the workflow described in
SKILL.md. - Boundary markers: None present in the instructions.
- Capability inventory: Shell execution of various bioinformatics tools and Python 3 scripts.
- Sanitization: No sanitization is applied to the raw genomic data before processing.
Audit Metadata