Motivation: The conversion of the raw intensities obtained from nextgeneration sequencing platforms into nucleotide sequences with wellcalibrated 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. Availability and implementation: FreeIbis is freely available for use under the GPL (http://bioinf.eva.mpg.de/freeibis/). It requires a Python interpreter and a Cþþ compiler. Tailored versions of LIBOCAS and LIBLINEAR are distributed along with the package. Contact: kelso@eva.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.
['Gabriel Renaud', 'Martin Kircher', 'Udo Stenzel', 'Janet Kelso']
freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers