DRAKKAR documentation

DRAKKAR is a modular, Snakemake-based workflow for genome-resolved metagenomics. It is designed for HPC use, re-entrant execution, and consistent output organization across preprocessing, cataloging, profiling, annotation, expression, and downstream troubleshooting workflows.

If you are new to DRAKKAR, start with Installation and then continue to the User guide guide.

Find what you need

If you want to…	Start here
Install DRAKKAR or prepare a working environment	See Installation for GitHub installation, HPC module use, and environment preparation.
Understand the basic input formats and how a run is organized	See User guide for quickstart commands, sample table structure, core concepts, and guide navigation.
Choose and run a workflow module	See Workflow guide for the complete workflow and all analysis modules such as preprocessing, cataloging, profiling, annotating, expressing, dereplicating, and inspecting.
Manage databases, logs, config, transfers, outputs, or troubleshooting	See Operations and troubleshooting for operational commands and maintenance tasks.
Check the command-line command list at a glance	See CLI Reference for the CLI reference.

Documentation map

Start here

• Installation
  • Install From GitHub
  • Use on Mjolnir (module)
  • Verify installation
  • Optional: pre-create environments
• User guide
  • Quickstart
  • Core concepts
  • Input formats
  • Guide map

Run workflows

• Workflow guide
  • Workflow overview
  • Complete workflow
  • Module reference
• Operations and troubleshooting
  • Operations overview
  • Database
  • Config
  • Snakemake and SLURM management
  • Status
  • Logging
  • Transfer
  • Maintenance commands
  • Outputs
  • Troubleshooting

Reference

• CLI Reference