The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill requires the 'pysam' library, specifically version 0.24.0, which is installed from a standard package registry. While the documentation notes that the underlying HTSlib components can optionally fetch genomic reference sequences from remote repositories (such as the EBI CRAM reference server), this is a standard feature in bioinformatics and is documented as disabled by default in the specified version.
[COMMAND_EXECUTION]: The bundled scripts (e.g., 'scripts/alignment_qc.py', 'scripts/filter_alignments.py') utilize the 'pysam.samtools' and 'pysam.bcftools' dispatchers to perform genomic operations. These dispatchers are used safely by passing command-line tokens as separate strings, which prevents shell injection. Furthermore, the skill provides helper functions in 'scripts/_common.py' that validate local file paths using the 'pathlib' library before processing begins.
[INDIRECT_PROMPT_INJECTION]: The skill processes untrusted genomic files (BAM, VCF, FASTA, etc.). While this represents an external data ingestion surface, the risk is mitigated by the fact that these are highly structured or binary formats processed by specialized HTSlib wrappers rather than direct natural language processing. The capability for the agent to write files or execute tools is restricted to the primary purpose of genomic analysis, and input data is not interpolated into system prompts.

pysam