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
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
