NAME
fastaq_to_perfect_reads
DESCRIPTION
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
AUTHOR
fastaq_to_perfect_reads was originally written by Martin Hunt ([email protected])
COPYING
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.