fastaq_to_perfect_reads (1)

fastaq_to_perfect_reads <fasta/q in> <out.fastq> <mean insert size> <insert std deviation> <mean coverage> <read length>

Makes perfect paired end fastq reads from a fasta/q 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 fasta/q file

outfile

Name of output fastq 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

fastaq_to_perfect_reads was originally written by Martin Hunt ([email protected])

Wellcome Trust Sanger Institute Copyright © 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.