RT Journal Article SR Electronic T1 Exploratory analysis and error modeling of a sequencing technology JF bioRxiv FD Cold Spring Harbor Laboratory SP 043042 DO 10.1101/043042 A1 Inouye, Michael A1 Small, Kerrin S. A1 Teo, Yik Y. A1 Li, Heng A1 Whiteford, Nava A1 Skelly, Tom A1 Abnizova, Irina A1 Turner, Daniel J. A1 Deloukas, Panos A1 Kwiatkowski, Dominic P. A1 Brown, Clive G. A1 Clark, Taane G. YR 2016 UL http://biorxiv.org/content/early/2016/03/13/043042.abstract AB Next generation DNA sequencing methods have created an unprecedented leap in sequence data generation, thus novel computational tools and statistical models are required to optimize and assess the resulting data. In this report, we explore underlying causes of error for the Illumina Genome Analyzer (IGA) sequencing technology and attempt to quantify their effects using a human bacterial artificial chromosome sequenced to 60,000 fold coverage. Seven potential error predictors are considered: Phred score, read entropy, tile coordinates, local tile density, base position within read, nucleotide call, and lane. With these parameters, logistic regression and log-linear models are constructed and used to show that each of the potential predictors contributes to error (P<1×10−4). With this additional information, we apply the logistic model and achieve a 3% improvement in both the sensitivity and specificity to detect IGA errors. Further, we demonstrate that these modeling approaches can be used as a feedback loop to inform laboratory methods and identify specific machine or run bias.