.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH FASTAQ-TO_PERFECT_READS "1" "July 2017" "fastaq 3.14.0" "User Commands"
.SH NAME
fastaq_to_perfect_reads \- Make perfect paired reads from reference
.SH DESCRIPTION
usage: fastaq_to_perfect_reads [options] <infile> <outfile> <mean insert size> <insert std deviation> <mean coverage> <read length>
.PP
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.
.SS "positional arguments:"
.TP
infile
Name of input file
.TP
outfile
Name of output file
.TP
mean insert size
Mean insert size of read pairs
.TP
insert std deviation
Standard devation of insert size
.TP
mean coverage
Mean coverage of the reads
.TP
read length
Length of each read
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-fragments\fR FILENAME
Write FASTA sequences of fragments (i.e. read pairs
plus sequences in between them) to the given filename
.TP
\fB\-\-no_n\fR
Don't allow any N or n characters in the reads
.TP
\fB\-\-seed\fR INT
Seed for random number generator. Default is to use
python's default