title: Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model.
abstract: BACKGROUND
  454 pyrosequencing is a commonly used massively parallel DNA sequencing technology with a wide variety of application fields such as epigenetics, metagenomics and transcriptomics. A well-known problem of this platform is its sensitivity to base-calling insertion and deletion errors, particularly in the presence of long homopolymers. In addition, the base-call quality scores are not informative with respect to whether an insertion or a deletion error is more likely. Surprisingly, not much effort has been devoted to the development of improved base-calling methods and more intuitive quality scores for this platform.
  
  
  RESULTS
  We present HPCall, a 454 base-calling method based on a weighted Hurdle Poisson model. HPCall uses a probabilistic framework to call the homopolymer lengths in the sequence by modeling well-known 454 noise predictors. Base-calling quality is assessed based on estimated probabilities for each homopolymer length, which are easily transformed to useful quality scores.
  
  
  CONCLUSIONS
  Using a reference data set of the Escherichia coli K-12 strain, we show that HPCall produces superior quality scores that are very informative towards possible insertion and deletion errors, while maintaining a base-calling accuracy that is better than the current one. Given the generality of the framework, HPCall has the potential to also adapt to other homopolymer-sensitive sequencing technologies.
authors.affiliation: Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Belgium. kristof.debeuf@ugent.be
authors.forename: Kristof De
authors.initials: KD
authors.lastname: Beuf
authors.forename: Joachim De
authors.initials: JD
authors.lastname: Schrijver
authors.forename: Olivier
authors.initials: O
authors.lastname: Thas
authors.forename: Wim Van
authors.initials: WV
authors.lastname: Criekinge
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Irizarry
authors.forename: Lieven
authors.initials: L
authors.lastname: Clement
mesh_terms: D048168:Escherichia coli K12 / Q000235:genetics; D016012:Poisson Distribution; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data*; D017384:Sequence Deletion