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PROGRAM:
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.
(c) Copyright 2009 by David Weese.
-h, --help
Displays this 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 NUM
Percent identity threshold. In range [50..100]. Default: 92.
-rr, --recognition-rate NUM
Percent recognition rate. In range [80..100]. Default: 99.
-pd, --param-dir DIR
Read user-computed parameter files in the directory <DIR>.
-id, --indels
Allow indels. Default: mismatches only.
-ll, --library-length NUM
Paired-end library length. In range [1..inf]. Default: 220.
-le, --library-error NUM
Paired-end library length tolerance. In range [0..inf]. Default: 50.
-m, --max-hits NUM
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 NUM
Trim reads to given length. Default: off. In range [14..inf].
-o, --output FILE
Change output filename. Default: <READS FILE>.razers. Valid filetypes are: razers,
eland, fa, fasta, and gff.
-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 NUM
Only consider matches with at most NUM more errors compared to the best. Default:
output all.
-gn, --genome-naming NUM
Select how genomes are named (see Naming section below). In range [0..1]. Default:
0.
-rn, --read-naming NUM
Select how reads are named (see Naming section below). In range [0..2]. Default: 0.
-so, --sort-order NUM
Select how matches are sorted (see Sorting section below). In range [0..1].
Default: 0.
-pf, --position-format NUM
Select begin/end position numbering (see Coordinate section below). In range
[0..1]. Default: 0.
Filtration Options:
-s, --shape BITSTRING
Manually set k-mer shape. Default: 11111111111.
-t, --threshold NUM
Manually set minimum k-mer count threshold. In range [1..inf].
-oc, --overabundance-cut NUM
Set k-mer overabundance cut ratio. In range [0..1].
-rl, --repeat-length NUM
Skip simple-repeats of length <NUM>. In range [1..inf]. Default: 1000.
-tl, --taboo-length NUM
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 FILE
Write error distribution to FILE.
-mcl, --min-clipped-len NUM
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
razers version: 1.2 [13764] Last update 2013-03-15
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