.TH RAZERS 1 "" "razers 1.5.8 [tarball]" ""
.SH NAME
razers \- Fast Read Mapping with Sensitivity Control
.SH SYNOPSIS
\fBrazers\fP [\fIOPTIONS\fP] <\fIGENOME FILE\fP> <\fIREADS FILE\fP>
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\fBrazers\fP [\fIOPTIONS\fP] <\fIGENOME FILE\fP> <\fIMP-READS FILE1\fP> <\fIMP-READS FILE2\fP>
.SH DESCRIPTION
RazerS is a versatile full-sensitive read mapper based on a k-mer counting filter. It supports single and paired-end mapping, and optimally parametrizes the filter based on a user-defined minimal sensitivity. See \fIhttp://www.seqan.de/projects/razers\fP for more information.
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Input to RazerS is a reference genome file and either one file with single-end reads or two files containing left or right mates of paired-end reads. Use - to read single-end reads from stdin.
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(c) Copyright 2009 by David Weese.
.SH REQUIRED ARGUMENTS
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\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.
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\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
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\fB-h\fP, \fB--help\fP
Display the help message.
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\fB--version\fP
Display version information.
.SS Main Options:
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\fB-f\fP, \fB--forward\fP
Map reads only to forward strands.
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\fB-r\fP, \fB--reverse\fP
Map reads only to reverse strands.
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\fB-i\fP, \fB--percent-identity\fP \fIDOUBLE\fP
Percent identity threshold. In range [50..100]. Default: \fI92\fP.
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\fB-rr\fP, \fB--recognition-rate\fP \fIDOUBLE\fP
Percent recognition rate. In range [80..100]. Default: \fI99\fP.
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\fB-pd\fP, \fB--param-dir\fP \fISTRING\fP
Read user-computed parameter files in the directory <\fIDIR\fP>.
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\fB-id\fP, \fB--indels\fP
Allow indels. Default: mismatches only.
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\fB-ll\fP, \fB--library-length\fP \fIINTEGER\fP
Paired-end library length. In range [1..inf]. Default: \fI220\fP.
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\fB-le\fP, \fB--library-error\fP \fIINTEGER\fP
Paired-end library length tolerance. In range [0..inf]. Default: \fI50\fP.
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\fB-m\fP, \fB--max-hits\fP \fIINTEGER\fP
Output only <\fINUM\fP> of the best hits. In range [1..inf]. Default: \fI100\fP.
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\fB--unique\fP
Output only unique best matches (-m 1 -dr 0 -pa).
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\fB-tr\fP, \fB--trim-reads\fP \fIINTEGER\fP
Trim reads to given length. Default: off. In range [14..inf].
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\fB-o\fP, \fB--output\fP \fIOUTPUT_FILE\fP
Change output filename (use - to dump to stdout in razers format). Default: <\fIREADS FILE\fP>.razers. Valid filetypes are: \fI.razers\fP, \fI.gff\fP, \fI.fasta\fP, \fI.fa\fP, and \fI.eland\fP.
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\fB-v\fP, \fB--verbose\fP
Verbose mode.
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\fB-vv\fP, \fB--vverbose\fP
Very verbose mode.
.SS Output Format Options:
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\fB-a\fP, \fB--alignment\fP
Dump the alignment for each match (only \fIrazer\fP or \fIfasta\fP format).
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\fB-pa\fP, \fB--purge-ambiguous\fP
Purge reads with more than <\fImax-hits\fP> best matches.
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\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.
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\fB-gn\fP, \fB--genome-naming\fP \fIINTEGER\fP
Select how genomes are named (see Naming section below). In range [0..1]. Default: \fI0\fP.
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\fB-rn\fP, \fB--read-naming\fP \fIINTEGER\fP
Select how reads are named (see Naming section below). In range [0..2]. Default: \fI0\fP.
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\fB-so\fP, \fB--sort-order\fP \fIINTEGER\fP
Select how matches are sorted (see Sorting section below). In range [0..1]. Default: \fI0\fP.
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\fB-pf\fP, \fB--position-format\fP \fIINTEGER\fP
Select begin/end position numbering (see Coordinate section below). In range [0..1]. Default: \fI0\fP.
.SS Filtration Options:
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\fB-s\fP, \fB--shape\fP \fISTRING\fP
Manually set k-mer shape. Default: \fI11111111111\fP.
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\fB-t\fP, \fB--threshold\fP \fIINTEGER\fP
Manually set minimum k-mer count threshold. In range [1..inf].
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\fB-oc\fP, \fB--overabundance-cut\fP \fIINTEGER\fP
Set k-mer overabundance cut ratio. In range [0..1].
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\fB-rl\fP, \fB--repeat-length\fP \fIINTEGER\fP
Skip simple-repeats of length <\fINUM\fP>. In range [1..inf]. Default: \fI1000\fP.
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\fB-tl\fP, \fB--taboo-length\fP \fIINTEGER\fP
Set taboo length. In range [1..inf]. Default: \fI1\fP.
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\fB-lm\fP, \fB--low-memory\fP
Decrease memory usage at the expense of runtime.
.SS Verification Options:
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\fB-mN\fP, \fB--match-N\fP
N matches all other characters. Default: N matches nothing.
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\fB-ed\fP, \fB--error-distr\fP \fISTRING\fP
Write error distribution to \fIFILE\fP.
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\fB-mcl\fP, \fB--min-clipped-len\fP \fIINTEGER\fP
Set minimal read length for read clipping. In range [0..inf]. Default: \fI0\fP.
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\fB-qih\fP, \fB--quality-in-header\fP
Quality string in fasta header.
.SH FORMATS, NAMING, SORTING, AND COORDINATE SCHEMES
RazerS supports various output formats. The output format is detected automatically from the file name suffix.
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\&.razers
Razer format
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\&.fa, .fasta
Enhanced Fasta format
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\&.eland
Eland format
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\&.gff
GFF format
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By default, reads and contigs are referred by their Fasta ids given in the input files. With the \fB-gn\fP and \fB-rn\fP options this behaviour can be changed:
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0
Use Fasta id.
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1
Enumerate beginning with 1.
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2
Use the read sequence (only for short reads!).
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The way matches are sorted in the output file can be changed with the \fB-so\fP option for the following formats: \fBrazer\fP, \fBfasta\fP, \fBsam\fP, and \fBamos\fP. Primary and secondary sort keys are:
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0
1. read number, 2. genome position
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1
1. genome position, 2. read number
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The coordinate space used for begin and end positions can be changed with the \fB-pf\fP option for the \fBrazer\fP and \fBfasta\fP formats:
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0
Gap space. Gaps between characters are counted from 0.
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1
Position space. Characters are counted from 1.
.SH EXAMPLES
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\fBrazers\fP \fBexample/genome.fa\fP \fBexample/reads.fa\fP \fB-id\fP \fB-a\fP \fB-mN\fP \fB-v\fP
Map single-end reads with 4% error rate, indels, and output the alignments. Ns are considered to match everything.
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\fBrazers\fP \fBexample/genome.fa\fP \fBexample/reads.fa\fP \fBexample/reads2.fa\fP \fB-id\fP \fB-mN\fP
Map paired-end reads with up to 4% errors, indels, and output concordantly mapped pairs within default library size. Ns are considered to match everything.