fastaq_long_read_simulate(1) simulates long reads from a fasta/q file


 fastaq_long_read_simulate [options] <infile> <outfile>

Simulates long reads from a fasta/q file. Can optionally make insertions into the reads, like pacbio does. If insertions made, coverage calculation is done before the insertions (so total read length may appear longer then expected).

positional arguments:

Name of input fasta/q file
Name of output fasta file

optional arguments:

-h, --help
show this help message and exit
--method tiling|uniform|gamma
How to sample the read positions and lengths. Choose from 1) "tiling", where reads of fixed length are taken at equal intervals from the reference. 2) "unfiform", where reads of fixed length taken at positions sampled uniformly. 3) "gamma", where reads lengths are taken from a gamma distribution, and positions sampled uniformly. [tiling]
--seed INT
Seed for random number generator [default: use python's default]
--qual INT
Write a file of fake quality scores called outfile.qual, all bases same quality [None]
--fixed_read_length INT
Length of each read. Only applies if method is tile or uniform. [20000]
--coverage FLOAT
Read coverage. Only applies if method is gamma or uniform. [2]

tiling options:

--tile_step INT
Distance between start of each read [10000]

gamma options:

--gamma_shape FLOAT
Shape parameter of gamma distribution [1.2]
--gamma_scale FLOAT
Scale parameter of gamma distribution [6000]
--gamma_min_length INT
Minimum read length [20000]

options to add insertions to reads:

--ins_skip INT
Insert a random base every --skip bases plus or minus --ins_window. If this option is used, must also use --ins_window.
--ins_window INT
See --ins_skip. If this option is used, must also use --ins_skip.


fastaq_long_read_simulate was originally written by Martin Hunt ([email protected])


Wellcome Trust Sanger Institute Copyright © 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.