title: freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers.
abstract: BACKGROUND
  The conversion of the raw intensities obtained from next-generation sequencing platforms into nucleotide sequences with well-calibrated quality scores is a critical step in the generation of good sequence data. While recent model-based approaches can yield highly accurate calls, they require a substantial amount of processing time and/or computational resources. We previously introduced Ibis, a fast and accurate basecaller for the Illumina platform. We have continued active development of Ibis to take into account developments in the Illumina technology, as well as to make Ibis fully open source.
  
  
  RESULTS
  We introduce here freeIbis, which offers significant improvements in sequence accuracy owing to the use of a novel multiclass support vector machine (SVM) algorithm. Sequence quality scores are now calibrated based on empirically observed scores, thus providing a high correlation to their respective error rates. These improvements result in downstream advantages including improved genotyping accuracy.
  
  
  METHODS
  FreeIbis is freely available for use under the GPL (http://bioinf.eva.mpg.de/freeibis/). It requires a Python interpreter and a C++ compiler. Tailored versions of LIBOCAS and LIBLINEAR are distributed along with the package.
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Renaud
authors.forename: Martin
authors.initials: M
authors.lastname: Kircher
authors.forename: Udo
authors.initials: U
authors.lastname: Stenzel
authors.forename: Janet
authors.initials: J
authors.lastname: Kelso
mesh_terms: D002138:Calibration; D060005:Genotyping Techniques / Q000592:standards; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000592:standards*; D012984:Software; D060388:Support Vector Machine