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

ARGUMENT 0 INPUT_FILE
    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.

READS List of INPUT_FILE's
    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

-h, --help
    Display the help message.

--version
    Display version information.

  Main Options:

-f, --forward
    Map reads only to forward strands.

-r, --reverse
    Map reads only to reverse strands.

-i, --percent-identity DOUBLE
    Percent identity threshold. In range [50..100]. Default: 92.

-rr, --recognition-rate DOUBLE
    Percent recognition rate. In range [80..100]. Default: 99.

-pd, --param-dir STRING
    Read user-computed parameter files in the directory <DIR>.

-id, --indels
    Allow indels. Default: mismatches only.

-ll, --library-length INTEGER
    Paired-end library length. In range [1..inf]. Default: 220.

-le, --library-error INTEGER
    Paired-end library length tolerance. In range [0..inf]. Default: 50.

-m, --max-hits INTEGER
    Output only <NUM> of the best hits. In range [1..inf]. Default: 100.

--unique
    Output only unique best matches (-m 1 -dr 0 -pa).

-tr, --trim-reads INTEGER
    Trim reads to given length. Default: off. In range [14..inf].

-o, --output OUTPUT_FILE
    Change output filename (use - to dump to stdout in razers format). Default: <READS FILE>.razers. Valid filetypes are: .razers, .gff, .fasta, .fa, and .eland.

-v, --verbose
    Verbose mode.

-vv, --vverbose
    Very verbose mode.

  Output Format Options:

-a, --alignment
    Dump the alignment for each match (only razer or fasta format).

-pa, --purge-ambiguous
    Purge reads with more than <max-hits> best matches.

-dr, --distance-range INTEGER
    Only consider matches with at most NUM more errors compared to the best. Default: output all.

-gn, --genome-naming INTEGER
    Select how genomes are named (see Naming section below). In range [0..1]. Default: 0.

-rn, --read-naming INTEGER
    Select how reads are named (see Naming section below). In range [0..2]. Default: 0.

-so, --sort-order INTEGER
    Select how matches are sorted (see Sorting section below). In range [0..1]. Default: 0.

-pf, --position-format INTEGER
    Select begin/end position numbering (see Coordinate section below). In range [0..1]. Default: 0.

  Filtration Options:

-s, --shape STRING
    Manually set k-mer shape. Default: 11111111111.

-t, --threshold INTEGER
    Manually set minimum k-mer count threshold. In range [1..inf].

-oc, --overabundance-cut INTEGER
    Set k-mer overabundance cut ratio. In range [0..1].

-rl, --repeat-length INTEGER
    Skip simple-repeats of length <NUM>. In range [1..inf]. Default: 1000.

-tl, --taboo-length INTEGER
    Set taboo length. In range [1..inf]. Default: 1.

-lm, --low-memory
    Decrease memory usage at the expense of runtime.

  Verification Options:

-mN, --match-N
    N matches all other characters. Default: N matches nothing.

-ed, --error-distr STRING
    Write error distribution to FILE.

-mcl, --min-clipped-len INTEGER
    Set minimal read length for read clipping. In range [0..inf]. Default: 0.

-qih, --quality-in-header
    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

razers example/genome.fa example/reads.fa -id -a -mN -v
    Map single-end reads with 4% error rate, indels, and output the alignments. Ns are considered to match everything.

razers example/genome.fa example/reads.fa example/reads2.fa -id -mN
    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.