# ONT Ecosystem Module Index

> Auto-generated by `ont_docgen.py generate` - v3.0.0

Cross-reference table linking lib/ modules to CLIs and skills.

## Module Overview

| Module | Purpose | Related CLI | Related Skills |
|--------|---------|-------------|----------------|
| `lib.advisory` | ONT Ecosystem Advisory Schema - Known issue adviso | `ont_qc_advisor.py` | qc-advisor |
| `lib.cache` | ONT Ecosystem Cache Utilities - Simple caching for | `-` | - |
| `lib.cli` | ONT Ecosystem CLI Utilities - Common CLI patterns  | `-` | - |
| `lib.config` | ONT Ecosystem Configuration Management | `ont_config.py` | - |
| `lib.conflict_resolver` | ONT Ecosystem Conflict Resolver - Multi-site regis | `-` | - |
| `lib.context_detector` | ONT Ecosystem Context Detector - Analyze context a | `-` | skill-orchestration |
| `lib.discovery_report` | Discovery Report Module for ONT Experiment Analysi | `ont_experiments.py` | ont-experiments-v2 |
| `lib.dorado_models` | ONT Ecosystem Dorado Model Management - Model regi | `ont_dorado.py` | dorado-bench-v2 |
| `lib.error_recovery` | ONT Ecosystem Error Recovery Engine - Intelligent  | `ont_doctor.py` | - |
| `lib.errors` | ONT Ecosystem Error Classes - Standardized excepti | `-` | - |
| `lib.io` | ONT Ecosystem I/O Utilities - File handling and da | `-` | - |
| `lib.logging_config` | ONT Ecosystem Logging Configuration | `-` | - |
| `lib.nl_query` | ONT Ecosystem Natural Language Query - Parse and e | `ont_query.py` | - |
| `lib.parallel` | ONT Ecosystem Parallel Processing Utilities | `-` | - |
| `lib.pipelines` | Pipeline definition and execution system for ont-e | `-` | - |
| `lib.qc_baseline` | QC Baseline Storage for Oxford Nanopore Sequencing | `ont_qc_advisor.py` | qc-advisor |
| `lib.qc_knowledge` | QC Knowledge Base for Oxford Nanopore Sequencing | `ont_qc_advisor.py` | qc-advisor |
| `lib.qc_recommender` | QC Recommendation Engine for Oxford Nanopore Seque | `ont_qc_advisor.py` | qc-advisor |
| `lib.qscore` | Q-score utility functions for Oxford Nanopore data | `ont_dorado.py` | dorado-bench-v2 |
| `lib.quick_analysis` | Quick Analysis Module for ONT Experiment Discovery | `end_reason.py` | end-reason |
| `lib.reflect_analyzer` | ONT Ecosystem Reflect Analyzer - Analyze learning  | `ont_reflect.py` | reflect |
| `lib.reflect_schema` | ONT Ecosystem Reflect Schema - Learning event sche | `ont_reflect.py` | reflect |
| `lib.reflect_store` | ONT Ecosystem Reflect Store - Persistent event sto | `ont_reflect.py` | reflect |
| `lib.registry_sync` | ONT Ecosystem Registry Sync Engine - Multi-site re | `-` | - |
| `lib.sample_data` | ONT Ecosystem Sample Data Generator - Synthetic da | `-` | - |
| `lib.site_config` | ONT Ecosystem Site Configuration - Multi-site regi | `-` | - |
| `lib.skill_improver` | ONT Ecosystem Skill Improver - Generate improvemen | `-` | skill-maker |
| `lib.skill_registry` | ONT Ecosystem Skill Registry - Discovery, loading, | `ont_install_skills.py` | skill-orchestration |
| `lib.skill_router` | ONT Ecosystem Skill Router - Route requests to app | `-` | skill-orchestration |
| `lib.skill_schema` | ONT Ecosystem Skill Schema Definition | `-` | - |
| `lib.skill_test_runner` | ONT Ecosystem Skill Test Runner - Automated test d | `-` | - |
| `lib.skill_updater` | ONT Ecosystem Skill Updater - Safe skill updates w | `-` | skill-maker |
| `lib.skill_validator` | ONT Ecosystem Skill Validator - Comprehensive skil | `-` | - |
| `lib.slurm_monitor` | ONT Ecosystem SLURM Job State Monitoring | `ont_slurm.py` | - |
| `lib.slurm_recovery` | ONT Ecosystem SLURM Job Recovery Engine | `ont_slurm.py` | - |
| `lib.stats` | Statistics module for ont-ecosystem. | `ont_stats.py` | - |
| `lib.sync_queue` | ONT Ecosystem Sync Queue - Persistent queue for of | `-` | - |
| `lib.sync_transport` | ONT Ecosystem Sync Transport - Multi-site registry | `-` | - |
| `lib.tasks` | Task queue system for ont-ecosystem. | `-` | - |
| `lib.timing` | ONT Ecosystem Timing Utilities | `-` | - |
| `lib.trigger_evaluator` | ONT Ecosystem Trigger Evaluator - Evaluate trigger | `-` | skill-orchestration |
| `lib.tutorial_engine` | ONT Ecosystem Tutorial Engine - Interactive lesson | `ont_tutorial.py` | - |
| `lib.tutorial_lessons` | ONT Ecosystem Tutorial Lessons - Structured lesson | `ont_tutorial.py` | - |
| `lib.tutorial_progress` | ONT Ecosystem Tutorial Progress Tracking | `ont_tutorial.py` | - |
| `lib.validation` | ONT Ecosystem Validation Utilities - Data validati | `ont_validate.py` | - |
| `lib.vector_clock` | ONT Ecosystem Vector Clock - Multi-site event caus | `-` | - |
| `lib.version` | Version management module for ont-ecosystem. | `ont_version.py` | - |

## Module Categories

### Core Utilities

- **`lib.config`**: ONT Ecosystem Configuration Management
- **`lib.cache`**: ONT Ecosystem Cache Utilities - Simple caching for expensive operations
- **`lib.io`**: ONT Ecosystem I/O Utilities - File handling and data serialization
- **`lib.logging_config`**: ONT Ecosystem Logging Configuration
- **`lib.timing`**: ONT Ecosystem Timing Utilities
- **`lib.parallel`**: ONT Ecosystem Parallel Processing Utilities
- **`lib.cli`**: ONT Ecosystem CLI Utilities - Common CLI patterns and helpers
- **`lib.errors`**: ONT Ecosystem Error Classes - Standardized exceptions and error handling
- **`lib.validation`**: ONT Ecosystem Validation Utilities - Data validation helpers

### Data Analysis

- **`lib.qscore`**: Q-score utility functions for Oxford Nanopore data.
- **`lib.stats`**: Statistics module for ont-ecosystem.
- **`lib.quick_analysis`**: Quick Analysis Module for ONT Experiment Discovery

### Experiment Management

- **`lib.discovery_report`**: Discovery Report Module for ONT Experiment Analysis

### Skill System

- **`lib.skill_registry`**: ONT Ecosystem Skill Registry - Discovery, loading, and management of skills
- **`lib.skill_router`**: ONT Ecosystem Skill Router - Route requests to appropriate skills
- **`lib.skill_improver`**: ONT Ecosystem Skill Improver - Generate improvement proposals for skills
- **`lib.skill_updater`**: ONT Ecosystem Skill Updater - Safe skill updates with git integration
- **`lib.skill_schema`**: ONT Ecosystem Skill Schema Definition
- **`lib.skill_validator`**: ONT Ecosystem Skill Validator - Comprehensive skill frontmatter validation
- **`lib.skill_test_runner`**: ONT Ecosystem Skill Test Runner - Automated test discovery and execution for skills

### Context & Triggers

- **`lib.context_detector`**: ONT Ecosystem Context Detector - Analyze context and identify relevant skills
- **`lib.trigger_evaluator`**: ONT Ecosystem Trigger Evaluator - Evaluate trigger conditions and rank skills

### Reflect/Learning

- **`lib.reflect_store`**: ONT Ecosystem Reflect Store - Persistent event storage for learning loop
- **`lib.reflect_analyzer`**: ONT Ecosystem Reflect Analyzer - Analyze learning events and generate insights
- **`lib.reflect_schema`**: ONT Ecosystem Reflect Schema - Learning event schema for skill improvement

### HPC Support

- **`lib.slurm_monitor`**: ONT Ecosystem SLURM Job State Monitoring
- **`lib.slurm_recovery`**: ONT Ecosystem SLURM Job Recovery Engine
- **`lib.dorado_models`**: ONT Ecosystem Dorado Model Management - Model registry and caching

### QC Advisory

- **`lib.advisory`**: ONT Ecosystem Advisory Schema - Known issue advisory system
- **`lib.qc_baseline`**: QC Baseline Storage for Oxford Nanopore Sequencing
- **`lib.qc_knowledge`**: QC Knowledge Base for Oxford Nanopore Sequencing
- **`lib.qc_recommender`**: QC Recommendation Engine for Oxford Nanopore Sequencing

### Tutorial System

- **`lib.tutorial_engine`**: ONT Ecosystem Tutorial Engine - Interactive lesson management
- **`lib.tutorial_lessons`**: ONT Ecosystem Tutorial Lessons - Structured lesson definitions
- **`lib.tutorial_progress`**: ONT Ecosystem Tutorial Progress Tracking

### Natural Language

- **`lib.nl_query`**: ONT Ecosystem Natural Language Query - Parse and execute natural language queries

### Version Control

- **`lib.version`**: Version management module for ont-ecosystem.