.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH SPLAZERS "1" "June 2017" "splazers 2.3.1+dfsg-4" "User Commands"
.SH NAME
splazers \- Split\-map read sequences
.PP
SYNOPSIS
.IP
splazers [OPTIONS] <GENOME FILE> <READS FILE>
splazers [OPTIONS] <GENOME FILE> <READS FILE 1> <READS FILE 2>
.PP
DESCRIPTION
.IP
SplazerS uses a prefix\-suffix mapping strategy to split\-map read
sequences.If a SAM file of mapped reads is given as input, all unmapped
but anchoredreads are split\-mapped onto anchoring target regions (specify
option \fB\-an\fR),if a Fasta/q file of reads is given, reads are split\-mapped
onto the wholereference sequence.
.IP
(c) Copyright 2010 by Anne\-Katrin Emde.
.PP
REQUIRED ARGUMENTS
.IP
ARGUMENT 0 INPUT_FILE
.IP
A reference genome file. Valid filetypes are: .sam, .raw, .gbk,
\&.frn, .fq, .fna, .ffn, .fastq, .fasta, .faa, .fa, .embl, and .bam.
.IP
READS List of INPUT_FILE's
.IP
Either one (single\-end) or two (paired\-end) read files. Valid
filetypes are: .sam, .raw, .gbk, .frn, .fq, .fna, .ffn, .fastq,
\&.fasta, .faa, .fa, .embl, and .bam.
.PP
OPTIONS
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Display the help message.
.HP
\fB\-\-version\-check\fR BOOL
.IP
Turn this option off to disable version update notifications of the
application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: 1.
.HP
\fB\-\-version\fR
.IP
Display version information.
.IP
Main Options::
.HP
\fB\-o\fR, \fB\-\-output\fR OUTPUT_FILE
.IP
Change output filename. Default: <READS FILE>.result.
.HP
\fB\-f\fR, \fB\-\-forward\fR
.IP
only compute forward matches
.HP
\fB\-r\fR, \fB\-\-reverse\fR
.IP
only compute reverse complement matches
.HP
\fB\-i\fR, \fB\-\-percent\-identity\fR DOUBLE
.IP
Percent identity threshold. In range [50..100]. Default: 92.
.HP
\fB\-rr\fR, \fB\-\-recognition\-rate\fR DOUBLE
.IP
set the percent recognition rate In range [80..100]. Default: 99.
.HP
\fB\-pd\fR, \fB\-\-param\-dir\fR STRING
.IP
Read user\-computed parameter files in the directory <DIR>.
.HP
\fB\-id\fR, \fB\-\-indels\fR
.IP
Allow indels. Default: mismatches only.
.HP
\fB\-ll\fR, \fB\-\-library\-length\fR INTEGER
.IP
Paired\-end library length. In range [1..inf]. Default: 220.
.HP
\fB\-le\fR, \fB\-\-library\-error\fR INTEGER
.IP
Paired\-end library length tolerance. In range [0..inf]. Default: 50.
.HP
\fB\-m\fR, \fB\-\-max\-hits\fR INTEGER
.IP
Output only <NUM> of the best hits. In range [1..inf]. Default: 100.
.HP
\fB\-\-unique\fR
.IP
Output only unique best matches (\fB\-m\fR 1 \fB\-dr\fR 0 \fB\-pa\fR).
.HP
\fB\-tr\fR, \fB\-\-trim\-reads\fR INTEGER
.IP
Trim reads to given length. Default: off. In range [14..inf].
.HP
\fB\-mcl\fR, \fB\-\-min\-clipped\-len\fR INTEGER
.IP
min. read length for read clipping In range [1..inf]. Default: 0.
.HP
\fB\-qih\fR, \fB\-\-quality\-in\-header\fR
.IP
quality string in fasta header
.HP
\fB\-ou\fR, \fB\-\-outputUnmapped\fR OUTPUT_FILE
.IP
output filename for unmapped reads
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
verbose mode
.HP
\fB\-vv\fR, \fB\-\-vverbose\fR
.IP
very verbose mode
.IP
Output Format Options::
.HP
\fB\-a\fR, \fB\-\-alignment\fR
.IP
dump the alignment for each match
.HP
\fB\-pa\fR, \fB\-\-purge\-ambiguous\fR
.IP
purge reads with more than max\-hits best matches
.HP
\fB\-dr\fR, \fB\-\-distance\-range\fR INTEGER
.IP
only consider matches with at most NUM more errors compared to the
best (default output all)
.HP
\fB\-of\fR, \fB\-\-output\-format\fR INTEGER
.IP
Set output format. 0 = RazerS, 1 = Enhanced Fasta, 2 = Eland, 3 =
GFF, 4 = SAM. In range [0..4].
.HP
\fB\-gn\fR, \fB\-\-genome\-naming\fR INTEGER
.IP
Select how genomes are named. 0 = use Fasta id, 1 = enumerate
beginning with 1. In range [0..1]. Default: 0.
.HP
\fB\-rn\fR, \fB\-\-read\-naming\fR INTEGER
.IP
Select how reads are named. 0 = use Fasta id, 1 = enumerate
beginning with 1. In range [0..1]. Default: 0.
.HP
\fB\-so\fR, \fB\-\-sort\-order\fR INTEGER
.IP
Select how matches are sorted. 0 = read number, 1 = genome position.
In range [0..1]. Default: 0.
.HP
\fB\-pf\fR, \fB\-\-position\-format\fR INTEGER
.IP
Select begin/end position numbering (see Coordinate section below).
0 = gap space, 1 = position space. In range [0..1]. Default: 0.
.IP
Split Mapping Options::
.HP
\fB\-sm\fR, \fB\-\-split\-mapping\fR INTEGER
.IP
min. match length for prefix/suffix mapping (to disable split
mapping, set to 0) Default: 18.
.HP
\fB\-maxG\fR, \fB\-\-max\-gap\fR INTEGER
.IP
max. length of middle gap Default: 10000.
.HP
\fB\-minG\fR, \fB\-\-min\-gap\fR INTEGER
.IP
min. length of middle gap (for edit distance mapping about 10% of
read length is recommended) Default: 0.
.HP
\fB\-ep\fR, \fB\-\-errors\-prefix\fR INTEGER
.IP
max. number of errors in prefix match Default: 1.
.HP
\fB\-es\fR, \fB\-\-errors\-suffix\fR INTEGER
.IP
max. number of errors in suffix match Default: 1.
.HP
\fB\-gl\fR, \fB\-\-genome\-len\fR INTEGER
.IP
genome length in Mb, for computation of expected number of random
matches In range [\-inf..10000]. Default: 3000.
.HP
\fB\-an\fR, \fB\-\-anchored\fR
.IP
anchored split mapping, only unmapped reads with mapped mates will
be considered, requires the reads to be given in SAM format
.HP
\fB\-pc\fR, \fB\-\-penalty\-c\fR INTEGER
.IP
percent of read length, used as penalty for split\-gap Default: 2.
.IP
Filtration Options::
.HP
\fB\-oc\fR, \fB\-\-overabundance\-cut\fR INTEGER
.IP
Set k\-mer overabundance cut ratio. In range [0..1].
.HP
\fB\-rl\fR, \fB\-\-repeat\-length\fR INTEGER
.IP
Skip simple\-repeats of length <NUM>. In range [1..inf]. Default:
1000.
.HP
\fB\-tl\fR, \fB\-\-taboo\-length\fR INTEGER
.IP
Set taboo length. In range [1..inf]. Default: 1.
.HP
\fB\-lm\fR, \fB\-\-low\-memory\fR
.IP
decrease memory usage at the expense of runtime
.IP
Verification Options:
.HP
\fB\-mN\fR, \fB\-\-match\-N\fR
.IP
N matches all other characters. Default: N matches nothing.
.HP
\fB\-ed\fR, \fB\-\-error\-distr\fR STRING
.IP
Write error distribution to FILE.
.PP
VERSION
.IP
Last update:
splazers version: 1.3.6 [tarball]
SeqAn version: 2.3.1