bwa-mem2-dna-aligner
Pass
Audited by Gen Agent Trust Hub on Oct 14, 2026
Risk Level: SAFEEXTERNAL_DOWNLOADSCOMMAND_EXECUTIONINDIRECT_PROMPT_INJECTION
Full Analysis
- [EXTERNAL_DOWNLOADS]: The skill downloads the
bwa-mem2alignment tool from its official GitHub repository and fetches reference genomes from established genomic databases, including the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI). - [COMMAND_EXECUTION]: The instructions involve executing standard bioinformatics command-line utilities such as
bwa-mem2,samtools,picard, andgatkto perform genomic data indexing, alignment, and quality assessment. - [INDIRECT_PROMPT_INJECTION]: The skill defines a workflow for processing external FASTQ sequencing data and utilizes shell variables for sample identifiers, representing a typical data ingestion surface for automated bioinformatics pipelines.
- Ingestion points: External FASTQ read files and user-defined sample names referenced in
SKILL.md. - Boundary markers: None present in the command templates.
- Capability inventory: Execution of external bioinformatics binaries and local Python script execution for metrics parsing.
- Sanitization: None performed on sample names or file paths in the provided templates.
Audit Metadata