usage: fastqSimulate -f reference.fasta -o output-prefix -l read-length ....
-f ref.fasta Use sequences in ref.fasta as the genome.
-o name Create outputs name.1.fastq and name.2.fastq (and maybe others).
-l len Create reads of length 'len' bases.
-n n Create 'n' reads (for -se) or 'n' pairs of reads (for -pe and -mp).
-x read-cov Set 'np' to create reads that sample the genome to 'read-cov' read coverage.
-X clone-cov Set 'np' to create reads that sample the genome to 'clone-cov' clone coverage.
-em err Reads will contain fraction mismatch error 'e' (0.01 == 1% error).
-ei err Reads will contain fraction insertion error 'e' (0.01 == 1% error).
-ed err Reads will contain fraction deletion error 'e' (0.01 == 1% error).
-seed s Seed randomness with 32-bit integer s.
-allowgaps Allow pairs to span N regions in the reference. By default, pairs
are not allowed to span a gap. Reads are never allowed to cover N's.
-allowns Allow reads to contain N regions. Implies -allowgaps
-nojunction For -mp, do not create chimeric junction reads. Create only fully PE or
fully MP reads.
-normal p Output a normal-oriented (both forward or both reverse) pair with
probability p. Only for -pe and -mp.
Create single-end reads.
-cc junkSize junkStdDev false
Create chimeric single-end reads. The chimer is formed from two uniformly
distributed positions in the reference. Some amount of random junk is inserted
at the junction. With probability 'false' the read is not chimeric, but still
the junk bases inserted in the middle.
-pe shearSize shearStdDev
Create paired-end reads, from fragments of size 'shearSize +- shearStdDev'.
-mp insertSize insertStdDev shearSize shearStdDev enrichment
Create mate-pair reads. The pairs will be 'insertSize +- insertStdDev'
apart. The circularized insert is then sheared into fragments of size
'shearSize +- shearStdDev'. With probability 'enrichment' the fragment
containing the junction is used to form the pair of reads. The junction
location is uniformly distributed through this fragment.
Reads are labeled as:
tMP - a MP pair
fMP - a PE pair
aMP - a MP pair with junction in the first read
bMP - a MP pair with junction in the second read
cMP - a MP pair with junction in both reads (the reads overlap)
Output QV's are the Sanger spec.
ERROR: No fasta file (-f) supplied.
ERROR: No output prefix (-o) supplied.
ERROR: No type (-se or -pe or -mp) selected.