Guide

The guide is the practical layer of the Algorithms path. It assumes you already understand FastQTools’ positioning and now need to turn that understanding into executable commands, configuration, and deployment work.

Suggested learning order

Stage	Question to answer	Recommended reading
First step	How do I complete the first successful run?	Getting Started
Second step	Which commands and parameters are available?	CLI Reference
Third step	How do parameters, environment variables, and defaults work together?	Configuration
Fourth step	How do I place it into containers, CI, or batch environments?	Deployment

What this group of pages solves

• It lets first-time readers complete one statistics or filtering task on the shortest path.
• It helps current users quickly find command syntax, configuration precedence, and deployment cautions.
• It gives maintainers user-facing workflow context before they move into developer documentation.

How to read it

If all you need is to get it running today, read Getting Started and CLI Reference in order. If you plan to freeze commands into scripts or platforms, continue into Configuration and Deployment. If you are preparing to understand internals, treat this section as the prerequisite context before moving into the Developer Guide.