MasonFragSequencing

Given a FASTA file with fragments, simulate sequencing thereof.

This program is a more lightweight version of mason_sequencing without support for the application of VCF and fragment sampling. Output of SAM is also not available. However, it uses the same code for the simulation of the reads as the more powerful mason_simulator.

You can use mason_frag_sequencing if you want to implement you rown fragmentation behaviour, e.g. if you have implemented your own bias models.

Web Documentation for 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]

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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.)

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