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A Benchmark of Entropy Coders for the Compression of Genome Sequencing Data

文献类型: 会议论文

第一作者: S. Casale-Brunet

作者: S. Casale-Brunet 1 ; P. Ribeca 2 ; C. Alberti 3 ; U. Ozturk 1 ; M. Mattavelli 1 ;

作者机构: 1.EPFL SCI STI MM, Ecole Polytechnique Federale de Lausanne, Switzerland

2.Biomathematics and Statistics Scotland, United Kingdom

3.Genom Sys SA, Switzerland

关键词: Sequential analysis;ISO Standards;Transform coding;Symbols;Genomics;Benchmark testing;Entropy

会议名称: Data Compression Conference

主办单位:

页码: 1-1

摘要: Genomic sequencing data contain three different data fields: read names, quality values, and nucleotide sequences. In this work, a variety of entropy encoders and com-pression algorithms were benchmarked in terms of compression-decompression rates and times separately for each data field as raw data from FASTQ files (implemented in the Fastq analysis script) and in MPEG-G uncompressed descriptor symbols de-coded from MPEG-G bitstreams (implemented in the symbols analysis script). The result of this benchmark is then compared to the performance of CABAC, which is the encoder used in first edition of the ISO /IEC MPEG-G standard for all types of descriptors, since CABAC was the best performing in terms of compression rates for the three types of data, thus providing overall better compression rates compared to other entropy coders in total. However, in some use cases encoding and decoding speed might be of higher interest than compression, and for specific datasets, types of data, or descriptor streams, other entropy coders might provide higher speed and/or better compression performance than CABAC.

分类号: tp311.56-53

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