MasonFragSequencing

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 to use for random number generator.

force-single-end

Force single-end simulation although --out-right is given.

seq-technology

Set sequencing technology to simulate.

seq-mate-orientation

Orientation for paired reads. See section Read Orientation below.

seq-strands

Strands to simulate from, only applicable to paired sequencing simulation.

embed-read-info

Whether or not to embed read information.

read-name-prefix

Read names will have this prefix.

enable-bs-seq

Enable BS-seq simulation.

bs-seq-protocol

Protocol to use for BS-Seq simulation.

bs-seq-conversion-rate

Conversion rate for unmethylated Cs to become Ts.

illumina-read-length

Read length for Illumina simulation.

illumina-prob-insert

Insert per-base probability for insertion in Illumina sequencing.

illumina-prob-deletion

Insert per-base probability for deletion in Illumina sequencing.

illumina-prob-mismatch-scale

Scaling factor for Illumina mismatch probability.

illumina-prob-mismatch

Average per-base mismatch probability in Illumina sequencing.

illumina-prob-mismatch-begin

Per-base mismatch probability of first base in Illumina sequencing.

illumina-prob-mismatch-end

Per-base mismatch probability of last base in Illumina sequencing.

illumina-position-raise

Point where the error curve raises in relation to read length.

illumina-quality-mean-begin

Mean PHRED quality for non-mismatch bases of first base in Illumina sequencing.

illumina-quality-mean-end

Mean PHRED quality for non-mismatch bases of last base in Illumina sequencing.

illumina-quality-stddev-begin

Standard deviation of PHRED quality for non-mismatch bases of first base in Illumina sequencing.

illumina-quality-stddev-end

Standard deviation of PHRED quality for non-mismatch bases of last base in Illumina sequencing.

illumina-mismatch-quality-mean-begin

Mean PHRED quality for mismatch bases of first base in Illumina sequencing.

illumina-mismatch-quality-mean-end

Mean PHRED quality for mismatch bases of last base in Illumina sequencing.

illumina-mismatch-quality-stddev-begin

Standard deviation of PHRED quality for mismatch bases of first base in Illumina sequencing.

illumina-mismatch-quality-stddev-end

Standard deviation of PHRED quality for mismatch bases of last base in Illumina sequencing.

sanger-read-length-model

The model to use for sampling the Sanger read length.

sanger-read-length-min

The minimal read length when the read length is sampled uniformly.

sanger-read-length-max

The maximal read length when the read length is sampled uniformly.

sanger-read-length-mean

The mean read length when the read length is sampled with normal distribution.

sanger-read-length-error

The read length standard deviation when the read length is sampled uniformly.

sanger-prob-mismatch-scale

Scaling factor for Sanger mismatch probability.

sanger-prob-mismatch-begin

Per-base mismatch probability of first base in Sanger sequencing.

sanger-prob-mismatch-end

Per-base mismatch probability of last base in Sanger sequencing.

sanger-prob-insertion-begin

Per-base insertion probability of first base in Sanger sequencing.

sanger-prob-insertion-end

Per-base insertion probability of last base in Sanger sequencing.

sanger-prob-deletion-begin

Per-base deletion probability of first base in Sanger sequencing.

sanger-prob-deletion-end

Per-base deletion probability of last base in Sanger sequencing.

sanger-quality-match-start-mean

Mean PHRED quality for non-mismatch bases of first base in Sanger sequencing.

sanger-quality-match-end-mean

Mean PHRED quality for non-mismatch bases of last base in Sanger sequencing.

sanger-quality-match-start-stddev

Mean PHRED quality for non-mismatch bases of first base in Sanger sequencing.

sanger-quality-match-end-stddev

Mean PHRED quality for non-mismatch bases of last base in Sanger sequencing.

sanger-quality-error-start-mean

Mean PHRED quality for erroneous bases of first base in Sanger sequencing.

sanger-quality-error-end-mean

Mean PHRED quality for erroneous bases of last base in Sanger sequencing.

sanger-quality-error-start-stddev

Mean PHRED quality for erroneous bases of first base in Sanger sequencing.

sanger-quality-error-end-stddev

Mean PHRED quality for erroneous bases of last base in Sanger sequencing.

454-read-length-model

The model to use for sampling the 454 read length.

454-read-length-min

The minimal read length when the read length is sampled uniformly.

454-read-length-max

The maximal read length when the read length is sampled uniformly.

454-read-length-mean

The mean read length when the read length is sampled with normal distribution.

454-read-length-stddev

The read length standard deviation when the read length is sampled with normal distribution.

454-no-sqrt-in-std-dev

For error model, if set then (sigma = k * r)) is used, otherwise (sigma = k * sqrt(r)).

454-proportionality-factor

Proportionality factor for calculating the standard deviation proportional to the read length.

454-background-noise-mean

Mean of lognormal distribution to use for the noise.

454-background-noise-stddev

Standard deviation of lognormal distribution to use for the noise.

Input Ports

Path to 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]

Path to file with Illumina error profile. The file must be a text file with floating point numbers separated by space, each giving a positional error rate. [txt,opt.]

FASTQ file to use for a template for left-end reads. [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.]

FASTQ file to use for a template for right-end reads. [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.]

Output Ports

Output of single-end/left end reads. [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]

Output of right reads. Giving this options enables paired-end simulation. [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

MasonFragSequencing Std Output

The text sent to standard out during the execution of MasonFragSequencing.

MasonFragSequencing Error Output

The text sent to standard error during the execution of MasonFragSequencing. (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:

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

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