ragout1
Chromosome assembly with multiple references
Usage
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
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).