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.