
# Documentation

The metagWGS documentation can be found in the following pages:

   * [Installation](installation.md)
      * The pipeline installation procedure.
   * [Usage](usage.md)
      * An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
   * [Output](output.md)
      * An overview of the different output files and directories produced by the pipeline.
   * [Use case](use_case.md) (WARNING: not up-to-date, needs to be updated)
      * A tutorial to learn how to launch the pipeline on a test dataset on [genologin cluster](http://bioinfo.genotoul.fr/).
   * [Functional tests](../functional_tests/README.md)
      * (for developers) A tool to launch a new version of the pipeline on curated input data and compare its results with known output.
