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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]

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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

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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: 2024-11-09

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