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Improved base calling for the Illumina Genome Analyzer using machine learning strategies

Martin Kircher, Udo Stenzel and Janet Kelso*

Author Affiliations

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, 04103 Leipzig, Germany

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Genome Biology 2009, 10:R83  doi:10.1186/gb-2009-10-8-r83

Published: 14 August 2009

Abstract

The Illumina Genome Analyzer generates millions of short sequencing reads. We present Ibis (Improved base identification system), an accurate, fast and easy-to-use base caller that significantly reduces the error rate and increases the output of usable reads. Ibis is faster and more robust with respect to chemistry and technology than other publicly available packages. Ibis is freely available under the GPL from http://bioinf.eva.mpg.de/Ibis/ webcite.