CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores.
CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores.
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DOI：
10.1109/itw.2016.7606808
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发表时间：
2016-09
期刊：
影响因子：
--
通讯作者：
Weissman T
中科院分区：
文献类型：
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作者：
Ochoa I;No A;Hernaez M;Weissman T
由于测序技术的进步和测序成本的大幅下降，大量的测序数据正在产生。许多数据由核苷酸和表明其可靠性的相应质量分数组成。后者更难压缩并且本身有噪声。因此，最近提出了质量分数的有损压缩来降低存储成本。此外，已经表明，在某些特定速率下，有损压缩可以实现与无损压缩数据相似的变体调用性能。我们提出了 CROMqs，一种新的有损质量分数压缩器，具有“无穷小连续可精炼性”的特性。此属性允许解码器迭代地解压缩数据，而无需在压缩之前与编码器就特定速率达成一致。该特性在实践中特别适用，因为在大多数情况下，有损压缩机应以何种速率运行的适当速率无法在压缩之前确定。此外，此属性在涉及基因组数据流的场景中可能会很有趣。 CROMqs 是文献中第一个用于质量分数的无穷小连续细化有损压缩器，我们表明它获得了与之前提出的算法相当的率失真性能。此外，我们还表明，CROMqs 在变体调用方面实现了与无损压缩数据相当的性能。
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 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. As a result, lossy compression of the quality scores has recently been proposed to alleviate the storage costs. Further, it has been shown that lossy compression, at some specific rates, can achieve a performance on variant calling similar to that achieved with the lossless compressed data. We propose CROMqs, a new lossy compressor for the quality scores with the property of “infinitesimal successive refinability”. This property allows the decoder to decompress the data iteratively without the need of agreeing with the encoder on a specific rate prior to compression. This characteristic is particularly amenable in practice, as in most cases the appropriate rate at which the lossy compressor should operate can not be established prior to compression. Further, this property can be of interest in scenarios involving streaming of genomic data. CROMqs is the first infinitesimal successive refinement lossy compressor for the quality scores in the literature, and we show that it obtains a comparable rate-distortion performance to previously proposed algorithms. Moreover, we also show that CROMqs achieves a comparable performance on variant calling to that of the lossless compressed data.