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CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores.
Ochoa, I; No, A; Hernaez, M; Weissman, T.
Afiliação
  • Ochoa I; Department of Electrical Engineering, Stanford University, Stanford CA 94305.
  • No A; Department of Electrical Engineering, Stanford University, Stanford CA 94305.
  • Hernaez M; Department of Electrical Engineering, Stanford University, Stanford CA 94305.
  • Weissman T; Department of Electrical Engineering, Stanford University, Stanford CA 94305.
Proc Inf Theory Workshop ; 2016: 121-125, 2016 Sep.
Article em En | MEDLINE | ID: mdl-29806047
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.

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Proc Inf Theory Workshop Ano de publicação: 2016 Tipo de documento: Article País de publicação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Proc Inf Theory Workshop Ano de publicação: 2016 Tipo de documento: Article País de publicação: Estados Unidos