NAME¶

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.

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.

OPTIONS

-h, --help

Display the help message.

--version-check BOOL

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.

--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.

VERSION

Last update: razers version: 1.5.6 [tarball] SeqAn version: 2.3.1