wtdbg-cns1

Usage

Overview

WTDBG-CNS: Consensuser for wtdbg Author: Jue Ruan <[email protected]> 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