This node is currently not available in KNIME v5.4 — instead we’re showing this page for KNIME v4.7. You can use the version menu in the title bar to permanently switch your preferred version. This will also show the link to the update site.

Razers3

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.

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

: 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]
: 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

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

Popular Predecessors

Popular Successors

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.)

Workflows

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.

Installation

To use this node in KNIME, install the extension SeqAn from the below update site following our NodePit Product and Node Installation Guide:

v4.7

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Plugin version: 2.4.1.202004061533

On NodePit since: 2022-12-06

Last update: 2024-12-23

KNIME versions: From v3.6 to v4.7

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!