现有的Illumina数据模拟软件有以下几种：

1. pIRS

piRS: Profile-based Illumina pair-end reads simulator. 是BGI开发出来的软件。使用C++和Perl编写，下载地址：ftp://ftp.genomics.org.cn/pub/pIRS/。pIRS同时提供了一个引入variants的工具，从而能模拟杂合基因组数据。

文献：Xuesong Hu,Jianying Yuan,Yujian Shi,Jianliang Lu,Binghang Liu,Zhenyu Li,Yanxiang Chen,Desheng Mu,Hao Zhang,Nan Li,Zhen Yue,Fan Bai,Heng Li,and Wei Fan。 pIRS: Profile-based Illumina pair-end reads simulator Bioinformatics (2012) 28 (11): 1533-1535
first published online April 15, 2012 doi:10.1093/bioinformatics/bts187

2. ART

ART能模拟Illumina, 454和SOLiD的这3中NGS数据，包括 single-end, paired-end和mate-pair三种类型的数据。ART是NIH开发出的软件。其官网网址为：http://www.niehs.nih.gov/research/resources/software/biostatistics/art/。现在ART支持Illumina MiSeq的数据模拟了。该软件更新较多较快。

Citation: Weichun Huang, Leping Li, Jason R Myers, and Gabor T Marth. ART: a next-generation sequencing read simulator, Bioinformatics (2012) 28 (4): 593-594

3. 其它软件

Wgsim from the Samtools package (Li et al., 2009)

MetaSim (Richter et al., 2008) for simulating metagenomic data

Mason (http://seqan.de/projects/mason.html) for both Illumina and 454 reads

SimSeq (https://github.com/jstjohn/SimSeq) for Illumina reads

FlowSim (Balzer et al., 2010) for 454 reads.

PBSIM: PacBio reads simulator–toward accurate genome assembly