wtpoa-cns1

Usage

Overview

WTPOA-CNS: Consensuser for wtdbg using PO-MSA Author: Jue Ruan <[email protected]> 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