pbsim - Online in the Cloud

PROGRAM:

NAME

pbsim - simulator for PacBio sequencing reads

SYNOPSIS

pbsim options <reference.fasta>

DESCRIPTION

The pbsim command produces simulated PacBio reads for reference FASTA sequence
<reference.fasta>.

Model files (parameters for the --model-qc option) can be found in the
/usr/share/pbsim/models directory.

OPTIONS

The options for pbsim can be divided into general, sampling-based and model-based
simulation options.

General options
--prefix
prefix of output files (sd).

--data-type
data type. CLR or CCS (CLR).

--depth
depth of coverage (CLR: 20.0, CCS: 50.0).

--length-min
minimum length (100).

--length-max
maximum length (CLR: 25000, CCS: 2500).

--accuracy-min
minimum accuracy (CLR: 0.75, CCS: fixed as 0.75). This option can be used only in
case of CLR.

--accuracy-max
maximum accuracy (CLR: 1.00, CCS: fixed as 1.00). This option can be used only in
case of CLR.

--difference-ratio
ratio of differences. substitution:insertion:deletion. Each value up to 1000 (CLR:
10:60:30, CCS:6:21:73).

--seed for a pseudorandom number generator (Unix time).

Options for sampling-based simulation
--sample-fastq
FASTQ format file to sample.

--sample-profile-id
sample-fastq (filtered) profile ID. When using --sample-fastq, profile is stored.
sample_profile_<ID>.fastq, and sample_profile_<ID>_.stats are created. When not
using --sample-fastq, profile is re-used. Note that when profile is used,
--length-min,max, --accuracy-min,max would be the same as the profile.

Options for model-based simulation
--model_qc
model of quality code.

--length-mean
mean of length model (CLR: 3000.0, CCS:450.0).

--length-sd
standard deviation of length model (CLR: 2300.0, CCS: 170.0).

--accuracy-mean
mean of accuracy model (CLR: 0.78, CCS: fixed as 0.98). This option can be used
only in case of CLR.

--accuracy-sd
standard deviation of accuracy model (CLR: 0.02, CCS: fixed as 0.02). This option
can be used only in case of CLR.

EXAMPLES

To run model-based simulation:

pbsim --data-type CLR \
--depth 20 \
--model_qc /usr/share/pbsim/models/model_qc_clr \
reference.fasta

In the example above, simulated read sequences are randomly sampled from a reference
sequence ("reference.fasta") and differences (errors) of the sampled reads are introduced.
Data type is CLR, and coverage depth is 20. If the reference sequence is multi-FASTA file,
the simulated data is created for each FASTA. Three output files are created for each
FASTA. "sd_0001.ref" is a single-FASTA file which is copied from the reference sequence.
"sd_0001.fastq" is a simulated read dataset in the FASTQ format. "sd_0001.maf" is a list
of alignments between reference sequence and simulated reads in the MAF format. The length
and accuracy of reads are simulated based on our model of PacBio read.

To run sampling-based simulation:

pbsim --data-type CLR \
--depth 20 \
--sample-fastq sample.fastq \
reference.fastaq

In the sampling-based simulation, read length and quality score are the same as those of a
read taken randomly in the sample PacBio dataset ("sample.fastq").

Use pbsim online using onworks.net services