.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH WTPOA-CNS "1" "April 2020" "wtpoa-cns 2.5" "User Commands"
.SH NAME
wtpoa-cns \- Consensuser for wtdbg using PO-MSA
.SH SYNOPSIS
.B wtpoa-cns
[\fI\,options\/\fR]
.SH DESCRIPTION
WTPOA\-CNS: Consensuser for wtdbg using PO\-MSA
Author: Jue Ruan <ruanjue@gmail.com>
Version: 2.5 (20190621)
.SH OPTIONS
.TP
\fB\-t\fR <int>
Number of threads, [4]
.HP
\fB\-d\fR <string> Reference sequences for SAM input, will invoke sorted\-SAM input mode
.TP
\fB\-u\fR <int>
XORed flags to handle SAM input. [0]
0x1: Only process reference regions present in/between SAM alignments
0x2: Don't fileter secondary/supplementary SAM records with flag (0x100 | 0x800)
.TP
\fB\-r\fR
Force to use reference mode
.HP
\fB\-p\fR <string> Similar with \fB\-d\fR, but translate SAM into wtdbg layout file
.HP
\fB\-i\fR <string> Input file(s) *.ctg.lay from wtdbg, +, [STDIN]
.IP
Or sorted SAM files when having \fB\-d\fR/\-p
.HP
\fB\-o\fR <string> Output files, [STDOUT]
.TP
\fB\-f\fR
Force overwrite
.TP
\fB\-j\fR <int>
Expected max length of node, or say the overlap length of two adjacent units in layout file, [1500] bp
overlap will be default to 1500(or 150 for sam\-sr) when having \fB\-d\fR/\-p, block size will be 2.5 * overlap
.TP
\fB\-b\fR <int>
Bonus for tri\-bases match, [0]
.TP
\fB\-M\fR <int>
Match score, [2]
.TP
\fB\-X\fR <int>
Mismatch score, [\-5]
.TP
\fB\-I\fR <int>
Insertion score, [\-2]
.TP
\fB\-D\fR <int>
Deletion score, [\-4]
.TP
\fB\-H\fR <float>
Homopolymer merge score used in dp\-call\-cns mode, [\-3]
.TP
\fB\-B\fR <expr>
Bandwidth in POA, [Wmin[,Wmax[,mat_rate]]], mat_rate = matched_bases/total_bases [64,1024,0.92]
Program will double bandwidth from Wmin to Wmax when mat_rate is lower than setting
.TP
\fB\-W\fR <int>
Window size in the middle of the first read for fast align remaining reads, [200]
If $W is negative, will disable fast align, but use the abs($W) as Band align score cutoff
.TP
\fB\-w\fR <int>
Min size of aligned size in window, [$W * 0.5]
.TP
\fB\-A\fR
Abort TriPOA when any read cannot be fast aligned, then try POA
.TP
\fB\-S\fR <int>
Shuffle mode, 0: don't shuffle reads, 1: by shared kmers, 2: subsampling. [1]
.TP
\fB\-R\fR <int>
Realignment bandwidth, 0: disable, [16]
.TP
\fB\-c\fR <int>
Consensus mode: 0, run\-length; 1, dp\-call\-cns, [0]
.TP
\fB\-C\fR <int>
Min count of bases to call a consensus base, [3]
.TP
\fB\-F\fR <float>
Min frequency of non\-gap bases to call a consensus base, [0.5]
.TP
\fB\-N\fR <int>
Max number of reads in PO\-MSA [20]
Keep in mind that I am not going to generate high accurate consensus sequences here
.HP
\fB\-x\fR <string> Presets, []
.TP
sam\-sr: polishs contigs from short reads mapping, accepts sorted SAM files
shorted for '\-j 50 \fB\-W\fR 0 \fB\-R\fR 0 \fB\-b\fR 1 \fB\-c\fR 1 \fB\-N\fR 50 \fB\-rS\fR 2'
.TP
\fB\-q\fR
Quiet
.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.