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**Generic Workflow Nodes for KNIME: SeqAn** version **2.3.2.201707261654** by **Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team**

Simulate NUM reads/pairs from the reference sequence IN.fa, potentially with variants from IN.vcf. In case that both -o and -or are given, write out paired-end data, if only -io is given, only single-end reads are simulated.

- 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.
- meth-seed
- Seed to use for methylation level random number generator.
- seed-spacing
- Offset for seeds to use when multi-threading.
- num-threads
- Number of threads to use.
- force-single-end
- Force single-end simulation although --out-right file is given.
- chunk-size
- Number of fragments to simulate in one batch.
- num-fragments
- Number of reads/pairs to simulate.
- 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.
- fragment-size-model
- The model to use for the fragment size simulation.
- fragment-min-size
- Smallest fragment size to use when using uniform fragment size simulation.
- fragment-max-size
- Largest fragment size to use when using uniform fragment size simulation.
- fragment-mean-size
- Mean fragment size for normally distributed fragment size simulation.
- fragment-size-std-dev
- Fragment size standard deviation when using normally distributed fragment size simulation.
- 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.

- FASTA file with methylation levels of the input file. [fa,fasta,opt.]
- Path to FASTA file to read the reference from. [fa,fasta]
- Path to the VCF file with variants to apply. [vcf,opt.]
- 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,fastq,fq.gz,fastq.gz,opt.]
- FASTQ file to use for a template for right-end reads. [fq,fastq,fq.gz,fastq.gz,opt.]

- Output of single-end/left end reads. [fa,fasta,fq,fastq,fq.gz,fastq.gz]
- Output of right reads. Giving this options enables paired-end simulation. [fa,fasta,fq,fastq,fq.gz,fastq.gz,Inactive]
- SAM/BAM file with alignments. [sam,bam,Inactive]

- MasonSimulator Std Output
- The text sent to standard out during the execution of MasonSimulator.
- MasonSimulator Error Output
- The text sent to standard error during the execution of MasonSimulator. (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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