NAME
wtdbg-cns - Consensuser for wtdbg
SYNOPSIS
wtdbg-cns [options]
DESCRIPTION
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
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.