The Agent Skills Directory

[SAFE]: The skill serves as a comprehensive guide for using scikit-bio, an established open-source library for biological data analysis. All code samples and workflows provided are standard for bioinformatics tasks.
[SAFE]: External references point to official and reputable sources, including the library's official documentation, the project GitHub repository, and the reference paper published in Nature Methods.
[EXTERNAL_DOWNLOADS]: The skill instructs the agent to install dependencies using standard package managers (uv, pip, conda). These are routine operations for setting up a Python scientific environment and target known, legitimate packages.
[SAFE]: The skill defines workflows that ingest external biological data files (FASTA, FASTQ, BIOM, Newick). This is the intended purpose of the tool and represents a standard data-processing surface.
Ingestion points: Methods such as skbio.DNA.read(), skbio.io.read(), and Table.read() found in SKILL.md and references/api_reference.md.
Boundary markers: Not explicitly defined in the provided code snippets.
Capability inventory: The skill uses standard file system tools (Read, Write, Edit) and Bash to manage data and execute Python scripts.
Sanitization: Relies on the internal parsing logic of the scikit-bio library.

scikit-bio