table of contents
other versions
- jessie 1.5.0-1
FASTAQ_TO_PERFECT_READS(1) | Fastaq executables | FASTAQ_TO_PERFECT_READS(1) |
NAME¶
fastaq_to_perfect_readsDESCRIPTION¶
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 (mh12@sanger.ac.uk)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.October 2014 | Fastaq |