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MasonMaterializer

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

Apply variants from IN.vcf to IN.fa and write the results to out.fa.

Web Documentation for MasonMaterializer

Options

version-check
Turn this option off to disable version update notifications of the application.
quiet
Low verbosity.
verbose
Higher verbosity.
very-verbose
Highest verbosity.
seed
Seed for random number generation.
meth-seed
Seed for methylation simulation random number generation.
haplotype-name-sep
String separating contig name from haplotype number.
methylation-levels
Enable methylation level simulation.
meth-cg-mu
Median of beta distribution for methylation level of CpG loci.
meth-cg-sigma
Standard deviation of beta distribution for methylation level of CpG loci.
meth-chg-mu
Median of beta distribution for methylation level of CHG loci.
meth-chg-sigma
Standard deviation of beta distribution for methylation level of CHG loci.
meth-chh-mu
Median of beta distribution for methylation level of CHH loci.
meth-chh-sigma
Standard deviation of beta distribution for methylation level of CHH loci.

Input Ports

Icon
FASTA file with methylation levels of the input 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,sam,sam.bgzf,sam.gz,bam,opt.]
Icon
Path to FASTA file to read the reference from. [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,sam,sam.bgzf,sam.gz,bam]
Icon
Path to the VCF file with variants to apply. [vcf,vcf.bgzf,vcf.gz,opt.]

Output Ports

Icon
Output of materialized contigs. [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,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
Icon
TSV file to write breakpoints in variants to. [tsv,txt]
Icon
FASTA file with methylation levels of the output 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,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]

Views

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

Installation

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

KNIME 4.3

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

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