fastaq_long_read_simulate: Fastaq_long_read

DESCRIPTION

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:

infile: Name of input fasta/q file
outfile: 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 (1)