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.