The Agent Skills Directory

[SAFE]: The skill provides a comprehensive guide for genomic annotation using Prokka, a well-established bioinformatics tool. All operations described are standard practices in computational biology.
[EXTERNAL_DOWNLOADS]: The skill instructs the user to install software using trusted package managers. It references official repositories for installation:
Conda/Mamba installation from conda-forge and bioconda channels.
Pip installation for biopython, pandas, and matplotlib from PyPI.
[COMMAND_EXECUTION]: The skill utilizes shell commands to run prokka and manage genomic data. These commands are local, transparent, and aligned with the skill's stated purpose of genome annotation.
[DATA_EXPOSURE]: File operations are restricted to local genomic data (FASTA, GFF, GenBank). No access to sensitive system files, credentials, or environment variables is requested.
[INDIRECT_PROMPT_INJECTION]: While the skill processes external data (FASTA assemblies), this data is structured for biological analysis and does not present a typical injection surface for agent instructions. Standard file parsing libraries like BioPython are used, which do not execute code within the data.

prokka-genome-annotation