BOL

The guides describe the function, syntax, and typical use-cases of the tools; for a complete list of parameters, run the tool’s shellscript or open it with a text editor. Most tools do not currently have a guide, but each has shellscripts with basic usage information. The “General Usage Guide” gives shared background information covering usage of all tools.

Installation

General Usage Guide

Data Preprocessing Guide

Specific Tool Guides:

• BBDuk
• BBMap
• BBMask
• BBMerge
• BBNorm
• CalcUniqueness
• Clumpify
• Dedupe
• Reformat
• Repair
• Seal
• Split Nextera
• Statistics
• Tadpole
• Taxonomy

https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/