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WTDBG-CNS(1) User Commands WTDBG-CNS(1)


wtdbg-cns - Consensuser for wtdbg


wtdbg-cns [options]


WTDBG-CNS: Consensuser for wtdbg Author: Jue Ruan <> Version: 1.1


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

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

-o <string> Output files, [STDOUT]

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]
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 wtdbg-cns 2.5