ragout(1)

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