Razers2

RazerS 2 is a versatile full-sensitive read mapper based on a k-mer counting filter. It supports single and paired-end mapping, 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 2 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 by David Weese.

Web Documentation for Razers2

Options

forward
Map reads only to forward strands.
reverse
Map reads only to reverse strands.
percent-identity
Percent identity threshold.
recognition-rate
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.
verbose
Verbose mode.
vverbose
Very verbose mode.
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).
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.
shape
Manually set k-mer shape.
threshold
Manually set minimum k-mer count threshold.
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

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

Output Ports

Icon
Change output 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

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Razers2 Std Output
The text sent to standard out during the execution of Razers2.
Razers2 Error Output
The text sent to standard error during the execution of Razers2. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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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
KNIME versions: From v3.6 to v4.7

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