.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.36.
.TH RAZERS "1" "September 2009" "RazerS version 1.0 20090710 [4739]" "User Commands"
.SH NAME
RazerS \- Fast Read Mapping with Sensitivity Control
.SH SYNOPSIS
.B razers
[\fIOPTION\fR]... \fI<GENOME FILE> <READS FILE>\fR
.SH DESCRIPTION
RazerS \- Fast Read Mapping with Sensitivity Control
.IP
razers [OPTION]... <GENOME FILE> <MP\-READS FILE1> <MP\-READS FILE2>
.TP
\fB\-h\fR,  \fB\-\-help\fR
displays this help message
.TP
\fB\-V\fR,  \fB\-\-version\fR
print version information
.SS "Main Options:"
.TP
\fB\-f\fR,  \fB\-\-forward\fR
only compute forward matches
.TP
\fB\-r\fR,  \fB\-\-reverse\fR
only compute reverse complement matches
.TP
\fB\-i\fR,  \fB\-\-percent\-identity\fR NUM
set the percent identity threshold (default 92)
.TP
\fB\-rr\fR, \fB\-\-recognition\-rate\fR NUM
set the percent recognition rate (default 99)
.TP
\fB\-pd\fR, \fB\-\-param\-dir\fR DIR
folder containing user\-computed parameter files (optional)
.TP
\fB\-id\fR, \fB\-\-indels\fR
allow indels (default: mismatches only)
.TP
\fB\-ll\fR, \fB\-\-library\-length\fR NUM
mate\-pair library length (default 220)
.TP
\fB\-le\fR, \fB\-\-library\-error\fR NUM
mate\-pair library length tolerance (default 50)
.TP
\fB\-m\fR,  \fB\-\-max\-hits\fR NUM
output only NUM of the best hits (default 100)
.TP
\fB\-\-unique\fR
output only unique best matches (\fB\-m\fR 1 \fB\-dr\fR 0 \fB\-pa\fR)
.TP
\fB\-tr\fR, \fB\-\-trim\-reads\fR NUM
trim reads to given length (default off)
.TP
\fB\-o\fR,  \fB\-\-output\fR FILE
change output filename (default <READS FILE>.result)
.TP
\fB\-v\fR,  \fB\-\-verbose\fR
verbose mode
.TP
\fB\-vv\fR, \fB\-\-vverbose\fR
very verbose mode
.SS "Output Format Options:"
.TP
\fB\-a\fR,  \fB\-\-alignment\fR
dump the alignment for each match
.TP
\fB\-pa\fR, \fB\-\-purge\-ambiguous\fR
purge reads with more than max\-hits best matches
.TP
\fB\-dr\fR, \fB\-\-distance\-range\fR NUM
only consider matches with at most NUM more errors compared to the best (default output all)
.TP
\fB\-of\fR, \fB\-\-output\-format\fR NUM
set output format (default 0)
0 = Razer format
1 = enhanced Fasta format
2 = Eland format
3 = GFF format
.TP
\fB\-gn\fR, \fB\-\-genome\-naming\fR NUM
select how genomes are named (default 0)
0 = use Fasta id
1 = enumerate beginning with 1
.TP
\fB\-rn\fR, \fB\-\-read\-naming\fR NUM
select how reads are named (default 0)
0 = use Fasta id
1 = enumerate beginning with 1
2 = use the read sequence (only for short reads!)
.TP
\fB\-so\fR, \fB\-\-sort\-order\fR NUM
select how matches are sorted (default 0)
0 = 1. read number, 2. genome position
1 = 1. genome position, 2. read number
.TP
\fB\-pf\fR, \fB\-\-position\-format\fR NUM
select begin/end position numbering (default 0)
0 = gap space
1 = position space
.SS "Filtration Options:"
.TP
\fB\-s\fR,  \fB\-\-shape\fR BITSTRING
set k\-mer shape (default 11111111111)
.TP
\fB\-t\fR,  \fB\-\-threshold\fR NUM
set minimum k\-mer threshold (default 1)
.TP
\fB\-oc\fR, \fB\-\-overabundance\-cut\fR NUM
set k\-mer overabundance cut ratio (default 1)
.TP
\fB\-rl\fR, \fB\-\-repeat\-length\fR NUM
set simple\-repeat length threshold (default 1000)
.TP
\fB\-tl\fR, \fB\-\-taboo\-length\fR NUM
set taboo length (default 1)
.SS "Verification Options:"
.TP
\fB\-mN\fR, \fB\-\-match\-N\fR
\&'N' matches with all other characters
.TP
\fB\-ed\fR, \fB\-\-error\-distr\fR FILE
write error distribution to FILE
.SH AUTHOR
.br
razers was written by David Weese.
.PP
This manual page was generated using html2man and polished by
Soeren Sonnenburg <sonne@debian.org>, for the Debian project
(but may be used by others).