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    Lossy Compression of Quality Values in Sequencing Data

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    Author
    Morales, Veronica Suaste
    Houghten, Sheridan
    Keyword
    Applied Mathematics
    Genetics
    Biotechnology
    Compression
    Sequencing
    Journal title
    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    Publication Volume
    18
    Publication Issue
    5
    Publication Begin page
    1958
    Publication End page
    1969
    
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    URI
    http://hdl.handle.net/10464/16888
    Abstract
    The dropping cost of sequencing human DNA has allowed for fast development of several projects around the world generating huge amounts of DNA sequencing data. This deluge of data has run up against limited storage space, a problem that researchers are trying to solve through compression techniques. In this study we address the compression of SAM files, the standard output files for DNA alignment. We specifically study lossy compression techniques used for quality values reported in the SAM file and analyze the impact of such lossy techniques on the CRAM format. We present a series of experiments using a data set corresponding to individual NA12878 with three different fold coverages. We introduce a new lossy model, dynamic binning, and compare its performance to other lossy techniques, namely Illumina binning, LEON and QVZ. We analyze the compression ratio when using CRAM and also study the impact of the lossy techniques on SNP calling. Our results show that lossy techniques allow a better CRAM compression ratio. Furthermore, we show that SNP calling performance is not negatively affected and may even be boosted.
    ae974a485f413a2113503eed53cd6c53
    10.1109/tcbb.2019.2959273
    Scopus Count
    Collections
    Computer Science

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