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  • Correspondence
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Quality score compression improves genotyping accuracy

Nature Biotechnology volume 33, pages 240–243 (2015)Cite this article

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To the Editor:

Most next-generation sequencing (NGS) quality scores are space intensive, redundant and often misleading. In this Correspondence, we recover quality information directly from sequence data using a compression tool named Quartz, rendering such scores redundant and yielding substantially better space and time efficiencies for storage and analysis. Quartz is designed to operate on NGS reads in FASTQ format, but it can be trivially modified to discard quality scores in other formats for which scores are paired with sequence information. Discarding 95% of quality scores resulted, counterintuitively, in improved SNP calling, implying that compression need not come at the expense of accuracy.

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Figure 1: Compressive quality scores using the Quartz algorithm.
Figure 2: Scaled ROC curves of genotyping accuracy.

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Acknowledgements

We thank L. Cowen and N. Daniels for helpful discussions and comments. Y.W.Y. gratefully acknowledges support from the Fannie and John Hertz Foundation. D.Y., J.P. and B.B. are partially supported by US National Institutes of Health grant GM108348.

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Authors and Affiliations

  1. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Y William Yu, Deniz Yorukoglu, Jian Peng & Bonnie Berger

  2. Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Y William Yu, Jian Peng & Bonnie Berger

Authors
  1. Y William Yu
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  2. Deniz Yorukoglu
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  3. Jian Peng
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  4. Bonnie Berger
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Correspondence to Bonnie Berger.

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Supplementary information

Supplementary Figures and Text

Supplementary Figures 1–12, Supplementary Tables 1–6 and Supplementary Methods (PDF 889 kb)

Supplementary Code

Source code for the Quartz software described and used in the manuscript (ZIP 23 kb)

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Yu, Y., Yorukoglu, D., Peng, J. et al. Quality score compression improves genotyping accuracy. Nat Biotechnol 33, 240–243 (2015). https://doi.org/10.1038/nbt.3170

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