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Splazers

Generic Workflow Nodes for KNIME: SeqAn version 2.3.2.201707261654 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

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.

Web Documentation for Splazers

Options

version-check
Turn this option off to disable version update notifications of the application.
forward
only compute forward matches
reverse
only compute reverse complement matches
percent-identity
Percent identity threshold.
recognition-rate
set the percent recognition rate
param-dir
Read user-computed parameter files in the directory <DIR>.
indels
Allow indels. Default: mismatches only.
library-length
Paired-end library length.
library-error
Paired-end library length tolerance.
max-hits
Output only <NUM> of the best hits.
unique
Output only unique best matches (-m 1 -dr 0 -pa).
trim-reads
Trim reads to given length. Default: off.
min-clipped-len
min. read length for read clipping
quality-in-header
quality string in fasta header
verbose
verbose mode
vverbose
very verbose mode
alignment
dump the alignment for each match
purge-ambiguous
purge reads with more than max-hits best matches
distance-range
only consider matches with at most NUM more errors compared to the best (default output all)
output-format
Set output format. 0 = RazerS, 1 = Enhanced Fasta, 2 = Eland, 3 = GFF, 4 = SAM.
genome-naming
Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1.
read-naming
Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1.
sort-order
Select how matches are sorted. 0 = read number, 1 = genome position.
position-format
Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space.
split-mapping
min. match length for prefix/suffix mapping (to disable split mapping, set to 0)
max-gap
max. length of middle gap
min-gap
min. length of middle gap (for edit distance mapping about 10% of read length is recommended)
errors-prefix
max. number of errors in prefix match
errors-suffix
max. number of errors in suffix match
genome-len
genome length in Mb, for computation of expected number of random matches
anchored
anchored split mapping, only unmapped reads with mapped mates will be considered, requires the reads to be given in SAM format
penalty-c
percent of read length, used as penalty for split-gap
overabundance-cut
Set k-mer overabundance cut ratio.
repeat-length
Skip simple-repeats of length <NUM>.
taboo-length
Set taboo length.
low-memory
decrease memory usage at the expense of runtime
match-N
N matches all other characters. Default: N matches nothing.
error-distr
Write error distribution to FILE.

Input Ports

A reference genome file. [fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam]
Either one (single-end) or two (paired-end) read files. [fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam,sam]

Output Ports

Change output filename. Default: <READS FILE>.result. [Inactive]
output filename for unmapped reads [Inactive]

Views

Splazers Std Output
The text sent to standard out during the execution of Splazers.
Splazers Error Output
The text sent to standard error during the execution of Splazers. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: SeqAn from the following update site:

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