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.