fastaq-to_perfect_reads1

Make perfect paired reads from reference

Overview

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

Releases

5 releases since Debian 9 (Stretch); the text changed 4 times.