Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model

Authors

Kristof De Beuf, Ghent University
Joachim De Schrijver, Ghent University
Olivier Thas, University of WollongongFollow
Wim Van Criekinge, Ghent University
Rafael A. Irizarry, Johns Hopkins Bloomberg School of Public Health
Lieven Clement, Ghent University

RIS ID

74976

Publication Details

De Beuf, K., De Schrijver, J., Thas, O., Van Criekinge, W., Irizarry, R. A. & Clement, L. (2012). Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. BMC Bioinformatics, 13 (303), 1-11.

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.