NGSimple

This pipeline, mainly written in perl is designed to simulate NGS
parameters (illumina sequencing type, read length, insert size and
coverage) based on a given reference, and give a report to choose
the best parameter combination that could contribute to a good
assembly.

simulation.pl generates simulated reads from a reference in fasta
format. It's recommended to start with a short reference (~5M
bases), in case that the number of generated reads is too large for
assembly.
input: reference + parameter
output: ./1.fastq/reads.fastq

assemly.pl assemble the reads (./1.fastq/reads.fastq) from those
designed libraries to assemblies. based on the parameters specified
in CONFIG file. It will generate assmblies with different K-mer
(./2.assembly/*), and choose the assembly with largest n50. Finally,
it will produce a quartile summary and mummerplot for each for you
to select a good parameter combination.

insert_size.pl will take real Illumina data as