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RAZERS(1) RAZERS(1)

NAME

razers - Fast Read Mapping with Sensitivity Control

SYNOPSIS

razers [OPTIONS] <GENOME FILE> <READS FILE>
razers [OPTIONS] <GENOME FILE> <MP-READS FILE1> <MP-READS FILE2>

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 http://www.seqan.de/projects/razers for more information.

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.

(c) Copyright 2009 by David Weese.

REQUIRED ARGUMENTS

A reference genome file. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.
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, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

OPTIONS

Display the help message.
Display version information.

Main Options:

Map reads only to forward strands.
Map reads only to reverse strands.
Percent identity threshold. In range [50..100]. Default: 92.
Percent recognition rate. In range [80..100]. Default: 99.
Read user-computed parameter files in the directory <DIR>.
Allow indels. Default: mismatches only.
Paired-end library length. In range [1..inf]. Default: 220.
Paired-end library length tolerance. In range [0..inf]. Default: 50.
Output only <NUM> of the best hits. In range [1..inf]. Default: 100.
Output only unique best matches (-m 1 -dr 0 -pa).
Trim reads to given length. Default: off. In range [14..inf].
Change output filename (use - to dump to stdout in razers format). Default: <READS FILE>.razers. Valid filetypes are: .razers, .gff, .fasta, .fa, and .eland.
Verbose mode.
Very verbose mode.

Output Format Options:

Dump the alignment for each match (only razer or fasta format).
Purge reads with more than <max-hits> best matches.
Only consider matches with at most NUM more errors compared to the best. Default: output all.
Select how genomes are named (see Naming section below). In range [0..1]. Default: 0.
Select how reads are named (see Naming section below). In range [0..2]. Default: 0.
Select how matches are sorted (see Sorting section below). In range [0..1]. Default: 0.
Select begin/end position numbering (see Coordinate section below). In range [0..1]. Default: 0.

Filtration Options:

Manually set k-mer shape. Default: 11111111111.
Manually set minimum k-mer count threshold. In range [1..inf].
Set k-mer overabundance cut ratio. In range [0..1].
Skip simple-repeats of length <NUM>. In range [1..inf]. Default: 1000.
Set taboo length. In range [1..inf]. Default: 1.
Decrease memory usage at the expense of runtime.

Verification Options:

N matches all other characters. Default: N matches nothing.
Write error distribution to FILE.
Set minimal read length for read clipping. In range [0..inf]. Default: 0.
Quality string in fasta header.

FORMATS, NAMING, SORTING, AND COORDINATE SCHEMES

RazerS supports various output formats. The output format is detected automatically from the file name suffix.

.razers
Razer format
.fa, .fasta
Enhanced Fasta format
.eland
Eland format
.gff
GFF format

By default, reads and contigs are referred by their Fasta ids given in the input files. With the -gn and -rn options this behaviour can be changed:

0
Use Fasta id.
1
Enumerate beginning with 1.
2
Use the read sequence (only for short reads!).

The way matches are sorted in the output file can be changed with the -so option for the following formats: razer, fasta, sam, and amos. Primary and secondary sort keys are:

0
1. read number, 2. genome position
1
1. genome position, 2. read number

The coordinate space used for begin and end positions can be changed with the -pf option for the razer and fasta formats:

0
Gap space. Gaps between characters are counted from 0.
1
Position space. Characters are counted from 1.

EXAMPLES

Map single-end reads with 4% error rate, indels, and output the alignments. Ns are considered to match everything.
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.
razers 1.5.8 [tarball]