Denoising of Quality Scores for Boosted Inference and Reduced Storage

Massive amounts of sequencing data are being generated thanks to advances in sequencing technology and a dramatic drop in the sequencing cost. Much of the raw data are comprised of nucleotides and the corresponding quality scores that indicate their reliability. The latter are more difficult to compress and are themselves noisy. Lossless and lossy compression of the quality scores has recently been proposed to alleviate the storage costs, but reducing the noise in the quality scores has remained largely unexplored. This raw data is processed in order to identify variants; these genetic variants are used in important applications, such as medical decision making. Thus improving the performance of the variant calling by reducing the noise contained in the quality scores is important. We propose a denoising scheme that reduces the noise of the quality scores and we demonstrate improved inference with this denoised data. Specifically, we show that replacing the quality scores with those generated by the proposed denoiser results in more accurate variant calling in general. Moreover, a consequence of the denoising is that the entropy of the produced quality scores is smaller, and thus significant compression can be achieved with respect to lossless compression of the original quality scores. We expect our results to provide a baseline for future research in denoising of quality scores. The code used in this work as well as a Supplement with all the results are available at http://web.stanford.edu/~iochoa/DCCdenoiser_CodeAndSupplement.zip.