---
name: "wtpoa-cns"
section: "1"
platform: "linux"
package: "wtdbg2"
version: "2.5-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/wtpoa-cns"
---

# wtpoa-cns(1)

Consensuser for wtdbg using PO-MSA

## NAME

wtpoa-cns - Consensuser for wtdbg using PO-MSA

## SYNOPSIS

**wtpoa-cns** \[*options*\]

## DESCRIPTION

WTPOA-CNS: Consensuser for wtdbg using PO-MSA Author: Jue Ruan \<ruanjue@gmail.com\> Version: 2.5 (20190621)

## OPTIONS

- **-t** \<int\>

  Number of threads, \[4\]

**-d** \<string\> Reference sequences for SAM input, will invoke sorted-SAM input mode

- **-u** \<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)

- **-r**

  Force to use reference mode

**-p** \<string\> Similar with **-d**, but translate SAM into wtdbg layout file

**-i** \<string\> Input file(s) \*.ctg.lay from wtdbg, +, \[STDIN\]

-

  Or sorted SAM files when having **-d**/-p

**-o** \<string\> Output files, \[STDOUT\]

- **-f**

  Force overwrite

- **-j** \<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 **-d**/-p, block size will be 2.5 \* overlap

- **-b** \<int\>

  Bonus for tri-bases match, \[0\]

- **-M** \<int\>

  Match score, \[2\]

- **-X** \<int\>

  Mismatch score, \[-5\]

- **-I** \<int\>

  Insertion score, \[-2\]

- **-D** \<int\>

  Deletion score, \[-4\]

- **-H** \<float\>

  Homopolymer merge score used in dp-call-cns mode, \[-3\]

- **-B** \<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

- **-W** \<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

- **-w** \<int\>

  Min size of aligned size in window, \[$W \* 0.5\]

- **-A**

  Abort TriPOA when any read cannot be fast aligned, then try POA

- **-S** \<int\>

  Shuffle mode, 0: don't shuffle reads, 1: by shared kmers, 2: subsampling. \[1\]

- **-R** \<int\>

  Realignment bandwidth, 0: disable, \[16\]

- **-c** \<int\>

  Consensus mode: 0, run-length; 1, dp-call-cns, \[0\]

- **-C** \<int\>

  Min count of bases to call a consensus base, \[3\]

- **-F** \<float\>

  Min frequency of non-gap bases to call a consensus base, \[0.5\]

- **-N** \<int\>

  Max number of reads in PO-MSA \[20\] Keep in mind that I am not going to generate high accurate consensus sequences here

**-x** \<string\> Presets, \[\]

- sam-sr: polishs contigs from short reads mapping, accepts sorted SAM files

  shorted for '-j 50 **-W** 0 **-R** 0 **-b** 1 **-c** 1 **-N** 50 **-rS** 2'

- **-q**

  Quiet

- **-v**

  Verbose

- **-V**

  Print version information and then exit

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.