Intensity normalization improves color calling in SOLiD sequencing.

Abstract

ABI’s SOLiD system is a commonly used massively parallel DNA sequencing platform for applications including genotyping and structural variation analysis to transcriptome quantification and reconstruction. Like other sequencing technologies, it measures fluorescence intensities from dye-labeled molecules to determine the sequence of DNA fragments. Ultimately, sequences are determined by complicated statistical manipulations of noisy intensity measurements but systematic biases may mislead downstream analysis. A number of proposed methods improve base-calling and quality metrics for other sequencing technologies^- and we now present Rsolid, software implementing an intensity normalization strategy for the SOLiD platform that substantially improves yield and accuracy at small computational costs (7% increase in total matches, 13% in perfect matches, 5% reduced error rate, and substantial reduction in false-positive SNP calls).