$ show GPTomics/bioSkills
bioSkills is a curated, archived collection of over 560 bioinformatics 'skills' designed to be consumed by AI coding agents (Claude Code, Codex CLI, etc.). Each skill consists of a SKILL.md containing expert guidance, a usage-guide.md, and one or more self-contained example scripts (Python, R, shell). The repository covers the full breadth of bioinformatics—from sequence manipulation, alignment, and variant calling to single-cell, spatial transcriptomics, and causal genomics. The examples are meticulously commented with version-pinned dependencies and explicit warnings against common pitfalls, reflecting a strong pedagogical focus. The repository is not a live application or library; it is a static knowledge base that has been archived with no further updates planned. Its primary value lies in the expert-compiled recipes and anti-pattern guidance that can steer AI-generated code toward correct methodology.
The LLM identified 2 files worth highlighting for reuse:
A well-structured installer script that sources a shared library (install-common.sh) and supports install, update, uninstall, dry-run, validate modes, category filtering, and project/workspace scope. It injects OpenClaw-specific YAML metadata via awk, performs rsync with exclusions, checks project conflicts, and verifies integrity via git commit hash. This pattern is reusable for packaging any hierarchical knowledge base or toolset into AI-agent skill environments.
Demonstrates synchronized iteration over paired-end FASTQ files with explicit handling of orphan reads—a common and tricky bioinformatics task. The code uses iterators, error messages, and a quality filtering example that gracefully handles unmatched pairs. This self-contained, well-commented script can be extracted and adapted for any project requiring robust paired-end FASTQ processing, especially where integration with external bioinformatics tools is needed.