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WTPOA-CNS(1) User Commands WTPOA-CNS(1)


wtpoa-cns - Consensuser for wtdbg using PO-MSA


wtpoa-cns [options]


WTPOA-CNS: Consensuser for wtdbg using PO-MSA Author: Jue Ruan <> Version: 2.5 (20190621)


-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)
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]

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]
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'
Print version information and then exit


This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
April 2020 wtpoa-cns 2.5