User Guide¶
This guide covers end-to-end usage scenarios for FastQTools, from quick start to advanced configuration.
Table of Contents¶
- Getting Started - Installation and first commands
- CLI Reference - Complete command-line reference
- Configuration - Configuration files and environment variables
- Deployment - Docker and production deployment
Quick Navigation¶
| Topic | Description |
|---|---|
| Getting Started | Installation, basic commands, first FASTQ processing |
| CLI Reference | All commands, flags, and examples |
| Configuration | YAML configuration, environment variables, precedence |
| Deployment | Docker images, production deployment, CI/CD integration |
Next Steps¶
- New users: Start with Getting Started
- Advanced users: See Configuration for advanced options
- Operators: Review Deployment for deployment best practices