NAME

fastaq_to_perfect_reads - Make perfect paired reads from reference

DESCRIPTION

usage: fastaq_to_perfect_reads [options] <infile> <outfile> <mean insert size> <insert std deviation> <mean coverage> <read length>

Makes perfect paired end fastq reads from a sequence file, with insert sizes sampled from a normal distribution. Read orientation is innies. Output is an interleaved FASTQ file.

positional arguments:

infile: Name of input file
outfile: Name of output file
mean insert size: Mean insert size of read pairs
insert std deviation: Standard devation of insert size
mean coverage: Mean coverage of the reads
read length: Length of each read

optional arguments:

-h, --help: show this help message and exit
--fragments FILENAME: Write FASTA sequences of fragments (i.e. read pairs plus sequences in between them) to the given filename
--no_n: Don't allow any N or n characters in the reads
--seed INT: Seed for random number generator. Default is to use python's default

April 2020

fastaq 3.17.0