NAME

       wtdbg-cns - Consensuser for wtdbg

SYNOPSIS

       wtdbg-cns [options]

DESCRIPTION

       WTDBG-CNS: Consensuser for wtdbg Author: Jue Ruan <ruanjue@gmail.com> Version: 1.1

OPTIONS

       -t <int>
              Number of threads, [1]

       -i <string> Input file(s) *.utg.cns from wtdbg, +, [STDIN]

       -o <string> Output files, [STDOUT]

       -f     Force overwrite

       -j <int>
              Expected  length  of  node, or say the overlap length of two adject units in layout
              file, [1000] bp


       -----------------BEG DBG options---------------------------------
       -k <int>
              Kmer size for long reads, [15]

       -Z <int>
              Z-cutoff, drop the lower  (score / <-X>), [4]

       -W <int>
              W-cutoff, drop the lagger (position), [48] In DAG correction, -W set the  bandwidth
              of alignment

       -H <int>
              High coverage bonus, [1]

       -L <int>
              High coverage cutoff = avg_cov / <-L> [10]

       -c <int>
              Candidate  strategy,  0: best-kmers, 1: median length, 2: first (include), 3: first
              (exclude), 4: longest, 5, shortest, [0] In DAG correction, force to use strategy 2


       -----------------END DBG options---------------------------------
       -M <int>
              Match score, [2]

       -X <int>
              Mismatch score, [-7]

       -I <int>
              Insertion score, [-3]

       -D <int>
              Deletion score, [-4]

       -E <int>
              Gap extension score, [-2]

       -m <int>
              1: DBG correction; 2: DAG correction, [1]

       -S <int>
              whether to correct structure before error correction, [1]

       -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.