.TH SPLAZERS 1 "" "splazers 1.3.7 [tarball]" ""
.SH NAME
splazers \- Split-map read sequences
.SH SYNOPSIS
\fBsplazers\fP [\fIOPTIONS\fP] <\fIGENOME FILE\fP> <\fIREADS FILE\fP>
.br
\fBsplazers\fP [\fIOPTIONS\fP] <\fIGENOME FILE\fP> <\fIREADS FILE 1\fP> <\fIREADS FILE 2\fP>
.SH DESCRIPTION
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 -an),if a Fasta/q file of reads is given, reads are split-mapped onto the wholereference sequence.
.sp
(c) Copyright 2010 by Anne-Katrin Emde.
.SH REQUIRED ARGUMENTS
.TP
\fBARGUMENT 0\fP \fIINPUT_FILE\fP
A reference genome file. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.gbk[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, \fI.embl[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.TP
\fBREADS\fP List of \fIINPUT_FILE\fP's
Either one (single-end) or two (paired-end) read files. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.gbk[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, \fI.embl[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
.TP
\fB--version\fP
Display version information.
.SS Main Options::
.TP
\fB-o\fP, \fB--output\fP \fIOUTPUT_FILE\fP
Change output filename. Default: <\fIREADS FILE\fP>.result.
.TP
\fB-f\fP, \fB--forward\fP
only compute forward matches
.TP
\fB-r\fP, \fB--reverse\fP
only compute reverse complement matches
.TP
\fB-i\fP, \fB--percent-identity\fP \fIDOUBLE\fP
Percent identity threshold. In range [50..100]. Default: \fI92\fP.
.TP
\fB-rr\fP, \fB--recognition-rate\fP \fIDOUBLE\fP
set the percent recognition rate In range [80..100]. Default: \fI99\fP.
.TP
\fB-pd\fP, \fB--param-dir\fP \fISTRING\fP
Read user-computed parameter files in the directory <\fIDIR\fP>.
.TP
\fB-id\fP, \fB--indels\fP
Allow indels. Default: mismatches only.
.TP
\fB-ll\fP, \fB--library-length\fP \fIINTEGER\fP
Paired-end library length. In range [1..inf]. Default: \fI220\fP.
.TP
\fB-le\fP, \fB--library-error\fP \fIINTEGER\fP
Paired-end library length tolerance. In range [0..inf]. Default: \fI50\fP.
.TP
\fB-m\fP, \fB--max-hits\fP \fIINTEGER\fP
Output only <\fINUM\fP> of the best hits. In range [1..inf]. Default: \fI100\fP.
.TP
\fB--unique\fP
Output only unique best matches (-m 1 -dr 0 -pa).
.TP
\fB-tr\fP, \fB--trim-reads\fP \fIINTEGER\fP
Trim reads to given length. Default: off. In range [14..inf].
.TP
\fB-mcl\fP, \fB--min-clipped-len\fP \fIINTEGER\fP
min. read length for read clipping In range [1..inf]. Default: \fI0\fP.
.TP
\fB-qih\fP, \fB--quality-in-header\fP
quality string in fasta header
.TP
\fB-ou\fP, \fB--outputUnmapped\fP \fIOUTPUT_FILE\fP
output filename for unmapped reads
.TP
\fB-v\fP, \fB--verbose\fP
verbose mode
.TP
\fB-vv\fP, \fB--vverbose\fP
very verbose mode
.SS Output Format Options::
.TP
\fB-a\fP, \fB--alignment\fP
dump the alignment for each match
.TP
\fB-pa\fP, \fB--purge-ambiguous\fP
purge reads with more than max-hits best matches
.TP
\fB-dr\fP, \fB--distance-range\fP \fIINTEGER\fP
only consider matches with at most NUM more errors compared to the best (default output all)
.TP
\fB-of\fP, \fB--output-format\fP \fIINTEGER\fP
Set output format. 0 = RazerS, 1 = Enhanced Fasta, 2 = Eland, 3 = GFF, 4 = SAM. In range [0..4].
.TP
\fB-gn\fP, \fB--genome-naming\fP \fIINTEGER\fP
Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: \fI0\fP.
.TP
\fB-rn\fP, \fB--read-naming\fP \fIINTEGER\fP
Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: \fI0\fP.
.TP
\fB-so\fP, \fB--sort-order\fP \fIINTEGER\fP
Select how matches are sorted. 0 = read number, 1 = genome position. In range [0..1]. Default: \fI0\fP.
.TP
\fB-pf\fP, \fB--position-format\fP \fIINTEGER\fP
Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space. In range [0..1]. Default: \fI0\fP.
.SS Split Mapping Options::
.TP
\fB-sm\fP, \fB--split-mapping\fP \fIINTEGER\fP
min. match length for prefix/suffix mapping (to disable split mapping, set to 0) Default: \fI18\fP.
.TP
\fB-maxG\fP, \fB--max-gap\fP \fIINTEGER\fP
max. length of middle gap Default: \fI10000\fP.
.TP
\fB-minG\fP, \fB--min-gap\fP \fIINTEGER\fP
min. length of middle gap (for edit distance mapping about 10% of read length is recommended) Default: \fI0\fP.
.TP
\fB-ep\fP, \fB--errors-prefix\fP \fIINTEGER\fP
max. number of errors in prefix match Default: \fI1\fP.
.TP
\fB-es\fP, \fB--errors-suffix\fP \fIINTEGER\fP
max. number of errors in suffix match Default: \fI1\fP.
.TP
\fB-gl\fP, \fB--genome-len\fP \fIINTEGER\fP
genome length in Mb, for computation of expected number of random matches In range [-inf..10000]. Default: \fI3000\fP.
.TP
\fB-an\fP, \fB--anchored\fP
anchored split mapping, only unmapped reads with mapped mates will be considered, requires the reads to be given in SAM format
.TP
\fB-pc\fP, \fB--penalty-c\fP \fIINTEGER\fP
percent of read length, used as penalty for split-gap Default: \fI2\fP.
.SS Filtration Options::
.TP
\fB-oc\fP, \fB--overabundance-cut\fP \fIINTEGER\fP
Set k-mer overabundance cut ratio. In range [0..1].
.TP
\fB-rl\fP, \fB--repeat-length\fP \fIINTEGER\fP
Skip simple-repeats of length <\fINUM\fP>. In range [1..inf]. Default: \fI1000\fP.
.TP
\fB-tl\fP, \fB--taboo-length\fP \fIINTEGER\fP
Set taboo length. In range [1..inf]. Default: \fI1\fP.
.TP
\fB-lm\fP, \fB--low-memory\fP
decrease memory usage at the expense of runtime
.SS Verification Options:
.TP
\fB-mN\fP, \fB--match-N\fP
N matches all other characters. Default: N matches nothing.
.TP
\fB-ed\fP, \fB--error-distr\fP \fISTRING\fP
Write error distribution to \fIFILE\fP.