.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH WTDBG-CNS "1" "April 2020" "wtdbg-cns 2.5" "User Commands"
.SH NAME
wtdbg-cns \- Consensuser for wtdbg
.SH SYNOPSIS
.B wtdbg-cns
[\fI\,options\/\fR]
.SH DESCRIPTION
WTDBG\-CNS: Consensuser for wtdbg
Author: Jue Ruan <ruanjue@gmail.com>
Version: 1.1
.SH OPTIONS
.TP
\fB\-t\fR <int>
Number of threads, [1]
.HP
\fB\-i\fR <string> Input file(s) *.utg.cns from wtdbg, +, [STDIN]
.HP
\fB\-o\fR <string> Output files, [STDOUT]
.TP
\fB\-f\fR
Force overwrite
.TP
\fB\-j\fR <int>
Expected length of node, or say the overlap length of two adject units in layout file, [1000] bp
.PP
\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-BEG\fR DBG options\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
.TP
\fB\-k\fR <int>
Kmer size for long reads, [15]
.TP
\fB\-Z\fR <int>
Z\-cutoff, drop the lower  (score / <\-X>), [4]
.TP
\fB\-W\fR <int>
W\-cutoff, drop the lagger (position), [48]
In DAG correction, \fB\-W\fR set the bandwidth of alignment
.TP
\fB\-H\fR <int>
High coverage bonus, [1]
.TP
\fB\-L\fR <int>
High coverage cutoff = avg_cov / <\-L> [10]
.TP
\fB\-c\fR <int>
Candidate strategy, 0: best\-kmers, 1: median length, 2: first (include), 3: first (exclude), 4: longest, 5, shortest, [0]
In DAG correction, force to use strategy 2
.PP
\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-END\fR DBG options\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
.TP
\fB\-M\fR <int>
Match score, [2]
.TP
\fB\-X\fR <int>
Mismatch score, [\-7]
.TP
\fB\-I\fR <int>
Insertion score, [\-3]
.TP
\fB\-D\fR <int>
Deletion score, [\-4]
.TP
\fB\-E\fR <int>
Gap extension score, [\-2]
.TP
\fB\-m\fR <int>
1: DBG correction; 2: DAG correction, [1]
.TP
\fB\-S\fR <int>
whether to correct structure before error correction, [1]
.TP
\fB\-v\fR
Verbose
.TP
\fB\-V\fR
Print version information and then 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.