Provided by: seqan-apps_2.4.0+dfsg-12ubuntu2_amd64 
NAME
mason_frag_sequencing - Fragment Sequencing Simulation
SYNOPSIS
mason_frag_sequencing [OPTIONS] -i IN.fa -o OUT.{fa,fq} [-or OUT2.{fa,fq}]
DESCRIPTION
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.
OPTIONS
-h, --help
Display the help message.
--version
Display version information.
-q, --quiet
Low verbosity.
-v, --verbose
Higher verbosity.
-vv, --very-verbose
Highest verbosity.
--seed INTEGER
Seed to use for random number generator. Default: 0.
-i, --in INPUT_FILE
Path to input file. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*],
.fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any
of the following extensions: gz, bz2, and bgzf for transparent (de)compression.
-o, --out OUTPUT_FILE
Output of single-end/left end reads. Valid filetypes are: .sam[.*], .raw[.*], .frn[.*], .fq[.*],
.fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], and .bam, where * is any of the
following extensions: gz, bz2, and bgzf for transparent (de)compression.
-or, --out-right OUTPUT_FILE
Output of right reads. Giving this options enables paired-end simulation. Valid filetypes are:
.sam[.*], .raw[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*],
.fa[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent
(de)compression.
--force-single-end
Force single-end simulation although --out-right is given.
Global Read Simulation Options:
--seq-technology STRING
Set sequencing technology to simulate. One of illumina, 454, and sanger. Default: illumina.
--seq-mate-orientation STRING
Orientation for paired reads. See section Read Orientation below. One of FR, RF, FF, and FF2.
Default: FR.
--seq-strands STRING
Strands to simulate from, only applicable to paired sequencing simulation. One of forward,
reverse, and both. Default: both.
--embed-read-info
Whether or not to embed read information.
--read-name-prefix STRING
Read names will have this prefix. Default: simulated..
BS-Seq Options:
--enable-bs-seq
Enable BS-seq simulation.
--bs-seq-protocol STRING
Protocol to use for BS-Seq simulation. One of directional and undirectional. Default: directional.
--bs-seq-conversion-rate DOUBLE
Conversion rate for unmethylated Cs to become Ts. In range [0..1]. Default: 0.99.
Illumina Options:
--illumina-read-length INTEGER
Read length for Illumina simulation. In range [1..inf]. Default: 100.
--illumina-error-profile-file INPUT_FILE
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. Valid filetype is: .txt.
--illumina-prob-insert DOUBLE
Insert per-base probability for insertion in Illumina sequencing. In range [0..1]. Default:
0.00005.
--illumina-prob-deletion DOUBLE
Insert per-base probability for deletion in Illumina sequencing. In range [0..1]. Default:
0.00005.
--illumina-prob-mismatch-scale DOUBLE
Scaling factor for Illumina mismatch probability. In range [0..inf]. Default: 1.0.
--illumina-prob-mismatch DOUBLE
Average per-base mismatch probability in Illumina sequencing. In range [0.0..1.0]. Default: 0.004.
--illumina-prob-mismatch-begin DOUBLE
Per-base mismatch probability of first base in Illumina sequencing. In range [0.0..1.0]. Default:
0.002.
--illumina-prob-mismatch-end DOUBLE
Per-base mismatch probability of last base in Illumina sequencing. In range [0.0..1.0]. Default:
0.012.
--illumina-position-raise DOUBLE
Point where the error curve raises in relation to read length. In range [0.0..1.0]. Default: 0.66.
--illumina-quality-mean-begin DOUBLE
Mean PHRED quality for non-mismatch bases of first base in Illumina sequencing. Default: 40.0.
--illumina-quality-mean-end DOUBLE
Mean PHRED quality for non-mismatch bases of last base in Illumina sequencing. Default: 39.5.
--illumina-quality-stddev-begin DOUBLE
Standard deviation of PHRED quality for non-mismatch bases of first base in Illumina sequencing.
Default: 0.05.
--illumina-quality-stddev-end DOUBLE
Standard deviation of PHRED quality for non-mismatch bases of last base in Illumina sequencing.
Default: 10.0.
--illumina-mismatch-quality-mean-begin DOUBLE
Mean PHRED quality for mismatch bases of first base in Illumina sequencing. Default: 40.0.
--illumina-mismatch-quality-mean-end DOUBLE
Mean PHRED quality for mismatch bases of last base in Illumina sequencing. Default: 30.0.
--illumina-mismatch-quality-stddev-begin DOUBLE
Standard deviation of PHRED quality for mismatch bases of first base in Illumina sequencing.
Default: 3.0.
--illumina-mismatch-quality-stddev-end DOUBLE
Standard deviation of PHRED quality for mismatch bases of last base in Illumina sequencing.
Default: 15.0.
--illumina-left-template-fastq INPUT_FILE
FASTQ file to use for a template for left-end reads. Valid filetypes are: .sam[.*], .raw[.*],
.gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*],
.embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent
(de)compression.
--illumina-right-template-fastq INPUT_FILE
FASTQ file to use for a template for right-end reads. Valid filetypes are: .sam[.*], .raw[.*],
.gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*],
.embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent
(de)compression.
Sanger Sequencing Options:
--sanger-read-length-model STRING
The model to use for sampling the Sanger read length. One of normal and uniform. Default: normal.
--sanger-read-length-min INTEGER
The minimal read length when the read length is sampled uniformly. In range [0..inf]. Default:
400.
--sanger-read-length-max INTEGER
The maximal read length when the read length is sampled uniformly. In range [0..inf]. Default:
600.
--sanger-read-length-mean DOUBLE
The mean read length when the read length is sampled with normal distribution. In range [0..inf].
Default: 400.
--sanger-read-length-error DOUBLE
The read length standard deviation when the read length is sampled uniformly. In range [0..inf].
Default: 40.
--sanger-prob-mismatch-scale DOUBLE
Scaling factor for Sanger mismatch probability. In range [0..inf]. Default: 1.0.
--sanger-prob-mismatch-begin DOUBLE
Per-base mismatch probability of first base in Sanger sequencing. In range [0.0..1.0]. Default:
0.005.
--sanger-prob-mismatch-end DOUBLE
Per-base mismatch probability of last base in Sanger sequencing. In range [0.0..1.0]. Default:
0.001.
--sanger-prob-insertion-begin DOUBLE
Per-base insertion probability of first base in Sanger sequencing. In range [0.0..1.0]. Default:
0.0025.
--sanger-prob-insertion-end DOUBLE
Per-base insertion probability of last base in Sanger sequencing. In range [0.0..1.0]. Default:
0.005.
--sanger-prob-deletion-begin DOUBLE
Per-base deletion probability of first base in Sanger sequencing. In range [0.0..1.0]. Default:
0.0025.
--sanger-prob-deletion-end DOUBLE
Per-base deletion probability of last base in Sanger sequencing. In range [0.0..1.0]. Default:
0.005.
--sanger-quality-match-start-mean DOUBLE
Mean PHRED quality for non-mismatch bases of first base in Sanger sequencing. Default: 40.0.
--sanger-quality-match-end-mean DOUBLE
Mean PHRED quality for non-mismatch bases of last base in Sanger sequencing. Default: 39.5.
--sanger-quality-match-start-stddev DOUBLE
Mean PHRED quality for non-mismatch bases of first base in Sanger sequencing. Default: 0.1.
--sanger-quality-match-end-stddev DOUBLE
Mean PHRED quality for non-mismatch bases of last base in Sanger sequencing. Default: 2.
--sanger-quality-error-start-mean DOUBLE
Mean PHRED quality for erroneous bases of first base in Sanger sequencing. Default: 30.
--sanger-quality-error-end-mean DOUBLE
Mean PHRED quality for erroneous bases of last base in Sanger sequencing. Default: 20.
--sanger-quality-error-start-stddev DOUBLE
Mean PHRED quality for erroneous bases of first base in Sanger sequencing. Default: 2.
--sanger-quality-error-end-stddev DOUBLE
Mean PHRED quality for erroneous bases of last base in Sanger sequencing. Default: 5.
454 Sequencing Options:
--454-read-length-model STRING
The model to use for sampling the 454 read length. One of normal and uniform. Default: normal.
--454-read-length-min INTEGER
The minimal read length when the read length is sampled uniformly. In range [0..inf]. Default: 10.
--454-read-length-max INTEGER
The maximal read length when the read length is sampled uniformly. In range [0..inf]. Default:
600.
--454-read-length-mean DOUBLE
The mean read length when the read length is sampled with normal distribution. In range [0..inf].
Default: 400.
--454-read-length-stddev DOUBLE
The read length standard deviation when the read length is sampled with normal distribution. In
range [0..inf]. Default: 40.
--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 DOUBLE
Proportionality factor for calculating the standard deviation proportional to the read length. In
range [0..inf]. Default: 0.15.
--454-background-noise-mean DOUBLE
Mean of lognormal distribution to use for the noise. In range [0..inf]. Default: 0.23.
--454-background-noise-stddev DOUBLE
Standard deviation of lognormal distribution to use for the noise. In range [0..inf]. Default:
0.15.
SEQUENCING SIMULATION
Simulation of base qualities is disabled when writing out FASTA files. Simulation of paired-end
sequencing is enabled when specifying two output files.
READ ORIENTATION
You can use the --mate-orientation to set the relative orientation when doing paired-end sequencing. The
valid values are given in the following.
FR Reads are inward-facing, the same as Illumina paired-end reads: R1 --> <-- R2.
RF Reads are outward-facing, the same as Illumina mate-pair reads: R1 <-- --> R2.
FF Reads are on the same strand: R1 --> --> R2.
FF2 Reads are on the same strand but the "right" reads are sequenced to the left of the "left" reads,
same as 454 paired: R2 --> --> R1.