[input]
fasta_dir=genome.fa

[output]
prefix=sim

# specify a seed (a non-negative integer) to reproduce the same output
# otherwise, comment out the following two lines.
[seed]
seed=0

[source_pool]
mrna_gtf=genes.gtf

[fragment]
length.mean=250
length.std_dev=40

# For num_fragments, use a slightly larger number of fragments than you need
# as the simulation program (tuxsim) may ultimately generate fewer fragments
# (for example, due to some transcript lengths being smaller than fragment lengths).
[sequencing]
read_length=100
num_fragments=22000000
max_edit_dist=3

[mismatch]
seq_error_per_bases=200