NAME

       ragout - Chromosome assembly with multiple references

SYNOPSIS

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

OPTIONS

   positional arguments:
       recipe_file
              path to recipe file

   optional arguments:
       -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

AUTHOR

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