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Open Access Highly Accessed Correspondence

Addressing challenges in the production and analysis of illumina sequencing data

Martin Kircher1, Patricia Heyn2 and Janet Kelso1*

Author Affiliations

1 Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics Deutscher Platz 6 04103 Leipzig, Germany

2 Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstrasse, 108 01307 Dresden, Germany

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BMC Genomics 2011, 12:382  doi:10.1186/1471-2164-12-382

Published: 29 July 2011

Abstract

Advances in DNA sequencing technologies have made it possible to generate large amounts of sequence data very rapidly and at substantially lower cost than capillary sequencing. These new technologies have specific characteristics and limitations that require either consideration during project design, or which must be addressed during data analysis. Specialist skills, both at the laboratory and the computational stages of project design and analysis, are crucial to the generation of high quality data from these new platforms. The Illumina sequencers (including the Genome Analyzers I/II/IIe/IIx and the new HiScan and HiSeq) represent a widely used platform providing parallel readout of several hundred million immobilized sequences using fluorescent-dye reversible-terminator chemistry. Sequencing library quality, sample handling, instrument settings and sequencing chemistry have a strong impact on sequencing run quality. The presence of adapter chimeras and adapter sequences at the end of short-insert molecules, as well as increased error rates and short read lengths complicate many computational analyses. We discuss here some of the factors that influence the frequency and severity of these problems and provide solutions for circumventing these. Further, we present a set of general principles for good analysis practice that enable problems with sequencing runs to be identified and dealt with.