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.

wtpoa-cns 2.5                                      April 2020                                       WTPOA-CNS(1)