NAME
fastaq_to_perfect_reads - Make perfect paired reads from reference
DESCRIPTION
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