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fastaq_to_perfect_reads - Make perfect paired reads from reference

FASTAQ-TO_PERFECT_READS(1) User Commands FASTAQ-TO_PERFECT_READS(1)

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
June 2017 fastaq 3.15.0