title: XS: a FASTQ read simulator.
abstract: BACKGROUND
  The emerging next-generation sequencing (NGS) is bringing, besides the natural huge amounts of data, an avalanche of new specialized tools (for analysis, compression, alignment, among others) and large public and private network infrastructures. Therefore, a direct necessity of specific simulation tools for testing and benchmarking is rising, such as a flexible and portable FASTQ read simulator, without the need of a reference sequence, yet correctly prepared for producing approximately the same characteristics as real data.
  
  
  RESULTS
  We present XS, a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. It has several running modes, depending on the time and memory available, and is aimed at testing computing infrastructures, namely cloud computing of large-scale projects, and testing FASTQ compression algorithms. Moreover, XS offers the possibility of simulating the three main FASTQ components individually (headers, DNA sequences and quality-scores).
  
  
  CONCLUSIONS
  XS provides an efficient and convenient method for fast simulation of FASTQ files, such as those from Ion Torrent (currently uncovered by other simulators), Roche-454, Illumina and ABI-SOLiD sequencing machines. This tool is publicly available at http://bioinformatics.ua.pt/software/xs/.
authors.affiliation: Signal Processing Lab, IEETA/DETI University of Aveiro, Aveiro 3810-193, Portugal. pratas@ua.pt.
authors.forename: Diogo
authors.initials: D
authors.lastname: Pratas
authors.forename: Armando J
authors.initials: AJ
authors.lastname: Pinho
authors.forename: João M O S
authors.initials: JM
authors.lastname: Rodrigues
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data*; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software