Nanopore quality score resolution can be reduced with little effect on downstream analysis

Abstract

We investigate the effect of quality score information loss on downstream analysis from nanopore sequencing FASTQ files. We polished denovo assemblies for a mock microbial community and a human genome, and we called variants on a human genome. We repeated these experiments using various pipelines, under various coverage level scenarios, and various quality score quantizers. In all cases we found that the quantization of quality scores cause little difference on (or even improves) the results obtained with the original (non-quantized) data. This suggests that the precision that is currently used for nanopore quality scores is unnecessarily high, and motivates the use of lossy compression algorithms for this kind of data. Moreover, we show that even a non-specialized compressor, like gzip, yields large storage space savings after quantization of quality scores.