The Agent Skills Directory

[COMMAND_EXECUTION]: The skill contains Python code snippets that utilize subprocess.run to call external bioinformatics CLI tools such as samtools, bamtools, and agp_validate. These calls are used for legitimate data processing and follow safe implementation practices.
[DATA_EXFILTRATION]: The documentation describes accessing the public GenomeArk S3 bucket. It correctly specifies the use of the --no-sign-request flag, which allows for data retrieval without exposing AWS credentials.
[PROMPT_INJECTION]: The skill outlines procedures for handling external data files, which technically creates an indirect prompt injection surface. However, the provided logic is focused on structural and coordinate-based validation, posing no significant risk of instruction override.

bioinformatics-fundamentals