title: pIRS: Profile-based Illumina pair-end reads simulator.
abstract: BACKGROUND
  The next-generation high-throughput sequencing technologies, especially from Illumina, have been widely used in re-sequencing and de novo assembly studies. However, there is no existing software that can simulate Illumina reads with real error and quality distributions and coverage bias yet, which is very useful in relevant software development and study designing of sequencing projects.
  
  
  RESULTS
  We provide a software package, pIRS (profile-based Illumina pair-end reads simulator), which simulates Illumina reads with empirical Base-Calling and GC%-depth profiles trained from real re-sequencing data. The error and quality distributions as well as coverage bias patterns of simulated reads using pIRS fit the properties of real sequencing data better than existing simulators. In addition, pIRS also comes with a tool to simulate the heterozygous diploid genomes.
  
  
  BACKGROUND
  pIRS is written in C++ and Perl, and is freely available at ftp://ftp.genomics.org.cn/pub/pIRS/.
authors.affiliation: BGI-Shenzhen, Shenzhen Biodynamic Optical Imaging Center, Peking University, Beijing, China.
authors.forename: Xuesong
authors.initials: X
authors.lastname: Hu
authors.forename: Jianying
authors.initials: J
authors.lastname: Yuan
authors.forename: Yujian
authors.initials: Y
authors.lastname: Shi
authors.forename: Jianliang
authors.initials: J
authors.lastname: Lu
authors.forename: Binghang
authors.initials: B
authors.lastname: Liu
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Li
authors.forename: Yanxiang
authors.initials: Y
authors.lastname: Chen
authors.forename: Desheng
authors.initials: D
authors.lastname: Mu
authors.forename: Hao
authors.initials: H
authors.lastname: Zhang
authors.forename: Nan
authors.initials: N
authors.lastname: Li
authors.forename: Zhen
authors.initials: Z
authors.lastname: Yue
authors.forename: Fan
authors.initials: F
authors.lastname: Bai
authors.forename: Heng
authors.initials: H
authors.lastname: Li
authors.forename: Wei
authors.initials: W
authors.lastname: Fan
mesh_terms: D003198:Computer Simulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016045:Human Genome Project; D006801:Humans; D008390:Markov Chains; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software