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Razers3

Generic Workflow Nodes for KNIME: SeqAn version 2.4.1.202004061533 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

RazerS 3 is a versatile full-sensitive read mapper based on k-mer counting and seeding filters. It supports single and paired-end mapping, shared-memory parallelism, 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 3 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 2009-2014 by David Weese.

Web Documentation for Razers3

Options

version-check
Turn this option off to disable version update notifications of the application.
percent-identity
Percent identity threshold.
recognition-rate
Percent recognition rate.
no-gaps
Allow only mismatches, no indels. Default: allow both.
forward
Map reads only to forward strands.
reverse
Map reads only to reverse strands.
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.
verbose
Verbose mode.
vverbose
Very verbose mode.
library-length
Paired-end library length.
library-error
Paired-end library length tolerance.
alignment
Dump the alignment for each match (only razer or fasta format).
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.
genome-naming
Select how genomes are named (see Naming section below).
read-naming
Select how reads are named (see Naming section below).
full-readid
Use the whole read id (don't clip after whitespace).
sort-order
Select how matches are sorted (see Sorting section below).
position-format
Select begin/end position numbering (see Coordinate section below).
dont-shrink-alignments
Disable alignment shrinking in SAM. This is required for generating a gold mapping for Rabema.
filter
Select k-mer filter.
mutation-rate
Set the percent mutation rate (pigeonhole).
overlap-length
Manually set the overlap length of adjacent k-mers (pigeonhole).
param-dir
Read user-computed parameter files in the directory <DIR> (swift).
threshold
Manually set minimum k-mer count threshold (swift).
taboo-length
Set taboo length (swift).
shape
Manually set k-mer shape.
overabundance-cut
Set k-mer overabundance cut ratio.
repeat-length
Skip simple-repeats of length <NUM>.
load-factor
Set the load factor for the open addressing k-mer index.
match-N
N matches all other characters. Default: N matches nothing.
error-distr
Write error distribution to FILE.
mismatch-file
Write mismatch patterns to FILE.
compact-mult
Multiply compaction threshold by this value after reaching and compacting.
no-compact-frac
Don't compact if in this last fraction of genome.
thread-count
Set the number of threads to use (0 to force sequential mode).
parallel-window-size
Collect candidates in windows of this length.
parallel-verification-size
Verify candidates in packages of this size.
parallel-verification-max-package-count
Largest number of packages to create for verification per thread-1.
available-matches-memory-size
Bytes of main memory available for storing matches.
match-histo-start-threshold
When to start histogram.

Input Ports

Icon
A reference genome file. [fq,fq.bgzf,fq.gz,fq.bz2,fastq,fastq.bgzf,fastq.gz,fastq.bz2,fa,fa.bgzf,fa.gz,fa.bz2,fasta,fasta.bgzf,fasta.gz,fasta.bz2,faa,faa.bgzf,faa.gz,faa.bz2,ffn,ffn.bgzf,ffn.gz,ffn.bz2,fna,fna.bgzf,fna.gz,fna.bz2,frn,frn.bgzf,frn.gz,frn.bz2,embl,embl.bgzf,embl.gz,embl.bz2,gbk,gbk.bgzf,gbk.gz,gbk.bz2,raw,raw.bgzf,raw.gz,raw.bz2,sam,sam.bgzf,sam.gz,sam.bz2,bam]
Icon
Either one (single-end) or two (paired-end) read files. [fq,fq.bgzf,fq.gz,fq.bz2,fastq,fastq.bgzf,fastq.gz,fastq.bz2,fa,fa.bgzf,fa.gz,fa.bz2,fasta,fasta.bgzf,fasta.gz,fasta.bz2,faa,faa.bgzf,faa.gz,faa.bz2,ffn,ffn.bgzf,ffn.gz,ffn.bz2,fna,fna.bgzf,fna.gz,fna.bz2,frn,frn.bgzf,frn.gz,frn.bz2,embl,embl.bgzf,embl.gz,embl.bz2,gbk,gbk.bgzf,gbk.gz,gbk.bz2,raw,raw.bgzf,raw.gz,raw.bz2,sam,sam.bgzf,sam.gz,sam.bz2,bam]

Output Ports

Icon
Mapping result filename (use - to dump to stdout in razers format). Default: <READS FILE>.razers. [razers,eland,fa,fasta,gff,sam,bam,afg]

Views

Razers3 Std Output
The text sent to standard out during the execution of Razers3.
Razers3 Error Output
The text sent to standard error during the execution of Razers3. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install SeqAn from the following update site:

KNIME 4.2

A zipped version of the software site can be downloaded here.

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