FASTAQ-TO_PERFECT_READS

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

options:

-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