0 ×

**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.)

To use this node in KNIME, install **Generic Workflow Nodes for KNIME: SeqAn** from the following update site:

Do you have feedback, questions, comments about NodePit, want to support this platform, or want your own nodes or workflows listed here as well? Do you think, the search results could be improved or something is missing? Then please get in touch! Alternatively, you can send us an email to mail@nodepit.com, follow @NodePit on Twitter, or chat on Gitter!

Please note that this is only about NodePit. We do not provide general support for KNIME — please use the KNIME forums instead.