fastaq_to_perfect_reads(1) Make perfect paired reads from reference


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:

Name of input file
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

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
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