title: Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim.
abstract: BACKGROUND
  The commercial launch of 454 pyrosequencing in 2005 was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to approximately 500 base pairs and are thus approaching read lengths obtained from traditional Sanger sequencing. Study design of sequencing projects would benefit from being able to simulate experiments.
  
  
  RESULTS
  We explore 454 raw data to investigate its characteristics and derive empirical distributions for the flow values generated by pyrosequencing. Based on our findings, we implement Flowsim, a simulator that generates realistic pyrosequencing data files of arbitrary size from a given set of input DNA sequences. We finally use our simulator to examine the impact of sequence lengths on the results of concrete whole-genome assemblies, and we suggest its use in planning of sequencing projects, benchmarking of assembly methods and other fields.
  
  
  BACKGROUND
  Flowsim is freely available under the General Public License from http://blog.malde.org/index.php/flowsim/.
authors.affiliation: Institute of Marine Research, University of Bergen, Bergen, Norway. susanne.balzer@imr.no
authors.forename: Susanne
authors.initials: S
authors.lastname: Balzer
authors.forename: Ketil
authors.initials: K
authors.lastname: Malde
authors.forename: Anders
authors.initials: A
authors.lastname: Lanzén
authors.forename: Animesh
authors.initials: A
authors.lastname: Sharma
authors.forename: Inge
authors.initials: I
authors.lastname: Jonassen
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D001492:Bass / Q000235:genetics; D002874:Chromosome Mapping; D003198:Computer Simulation; D004269:DNA, Bacterial; D001330:Electronic Data Processing; D004926:Escherichia coli / Q000235:genetics; D023281:Genomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods*
chemical_list: D004269:DNA, Bacterial
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