Arachne is run through through the use of executable modules, which are located in ARACHNE_BIN_DIR after a successful compilation. To run a module, simply type its name at the command line (you may need to run from ARACHNE_BIN_DIR if your PATH environment variable is not set correctly.) Each module accepts a set of command-line arguments specifying the details of its execution. See Executable modules for more details on running modules.
For a de novo assembly process, the first module you will want to run is Assemblez, a script module that conveniently runs many other modules in a logical pipeline. Assemblez may take several days, or even weeks, depending on the size and complexity of your genome. See Assemblez for more details. Note that you do NOT want to run Assemble.
For an assisted assembly process, see Assisted assembly.
After running Assemblez, you will be concerned with improving your assembly.