This is the command splazers that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
splazers ========
SYNOPSIS
splazers [OPTIONS] <GENOME FILE> <READS FILE> splazers [OPTIONS] <GENOME FILE>
<READS FILE 1> <READS FILE 2>
DESCRIPTION
SplazerS uses a prefix-suffix mapping strategy to split-map read sequences.If a SAM
file of mapped reads is given as input, all unmapped but anchoredreads are
split-mapped onto anchoring target regions (specify option -an),if a Fasta/q file
of reads is given, reads are split-mapped onto the wholereference sequence.
(c) Copyright 2010 by Anne-Katrin Emde.
-h, --help
Displays this help message.
--version
Display version information
Main Options::
-o, --output FILE
Change output filename. Default: <READS FILE>.result.
-f, --forward
only compute forward matches
-r, --reverse
only compute reverse complement matches
-i, --percent-identity NUM
Percent identity threshold. In range [50..100]. Default: 92.
-rr, --recognition-rate NUM
set the 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].
-mcl, --min-clipped-len NUM
min. read length for read clipping In range [1..inf]. Default: 0.
-qih, --quality-in-header
quality string in fasta header
-ou, --outputUnmapped FILE
output filename for unmapped reads
-v, --verbose
verbose mode
-vv, --vverbose
very verbose mode
Output Format Options::
-a, --alignment
dump the alignment for each match
-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)
-of, --output-format NUM
Set output format. 0 = RazerS, 1 = Enhanced Fasta, 2 = Eland, 3 = GFF, 4 = SAM. In
range [0..4].
-gn, --genome-naming NUM
Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In
range [0..1]. Default: 0.
-rn, --read-naming NUM
Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In
range [0..1]. Default: 0.
-so, --sort-order NUM
Select how matches are sorted. 0 = read number, 1 = genome position. In range
[0..1]. Default: 0.
-pf, --position-format NUM
Select begin/end position numbering (see Coordinate section below). 0 = gap space,
1 = position space. In range [0..1]. Default: 0.
Split Mapping Options::
-sm, --split-mapping NUM
min. match length for prefix/suffix mapping (to disable split mapping, set to 0)
Default: 18.
-maxG, --max-gap NUM
max. length of middle gap Default: 10000.
-minG, --min-gap NUM
min. length of middle gap (for edit distance mapping about 10% of read length is
recommended) Default: 0.
-ep, --errors-prefix NUM
max. number of errors in prefix match Default: 1.
-es, --errors-suffix NUM
max. number of errors in suffix match Default: 1.
-gl, --genome-len NUM
genome length in Mb, for computation of expected number of random matches In range
[-inf..10000]. Default: 3000.
-an, --anchored
anchored split mapping, only unmapped reads with mapped mates will be considered,
requires the reads to be given in SAM format
-pc, --penalty-c NUM
percent of read length, used as penalty for split-gap Default: 2.
Filtration Options::
-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.
VERSION
splazers version: 1.1 Last update Apr 2011
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