ragout - Chromosome assembly with multiple references

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

ragout 2.1.1                                      February 2019                                        RAGOUT(1)

       ragout - Chromosome assembly with multiple references

positionalarguments:
       recipe_file
              path to recipe file

   optionalarguments:-h, --help
              show this help message and exit

       -o output_dir, --outdir output_dir
              output directory (default: ragout-out)

       -s {sibelia,maf,hal}, --synteny {sibelia,maf,hal}
              backend for synteny block decomposition (default: sibelia)

       --refine
              enable refinement with assembly graph (default: False)

       --solid-scaffolds
              do not break input sequences - disables chimera detection module (default: False)

       --overwrite
              overwrite results from the previous run (default: False)

       --repeats
              enable repeat resolution algorithm (default: False)

       --debug
              enable debug output (default: False)

       -t THREADS, --threads THREADS
              number of threads for synteny backend (default: 1)

       --version
              show program's version number and exit

ragout   [-h]   [-o  output_dir]  [-s  {sibelia,maf,hal}]  [--refine]  [--solid-scaffolds]  [--overwrite]
       [--repeats] [--debug] [-t THREADS] [--version] recipe_file