.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH RAGOUT "1" "February 2019" "ragout 2.1.1" "User Commands"
.SH NAME
ragout \- Chromosome assembly with multiple references
.SH SYNOPSIS
.B ragout
[\-h] [\-o output_dir] [\-s {sibelia,maf,hal}] [\-\-refine]
[\-\-solid\-scaffolds] [\-\-overwrite] [\-\-repeats] [\-\-debug]
[\-t THREADS] [\-\-version]
recipe_file
.SH OPTIONS
.SS "positional arguments:"
.TP
recipe_file
path to recipe file
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-o\fR output_dir, \fB\-\-outdir\fR output_dir
output directory (default: ragout\-out)
.TP
\fB\-s\fR {sibelia,maf,hal}, \fB\-\-synteny\fR {sibelia,maf,hal}
backend for synteny block decomposition (default:
sibelia)
.TP
\fB\-\-refine\fR
enable refinement with assembly graph (default: False)
.TP
\fB\-\-solid\-scaffolds\fR
do not break input sequences \- disables chimera
detection module (default: False)
.TP
\fB\-\-overwrite\fR
overwrite results from the previous run (default:
False)
.TP
\fB\-\-repeats\fR
enable repeat resolution algorithm (default: False)
.TP
\fB\-\-debug\fR
enable debug output (default: False)
.TP
\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
number of threads for synteny backend (default: 1)
.TP
\fB\-\-version\fR
show program's version number and exit
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.