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GABAC: an arithmetic coding solution for genomic data
(Oxford University Press, 2020) Hernaez, M. (Mikel); Voges, J. (Jan); Paridaens, T. (Tom); Müntefering, F. (Fabian); Mainzer, L.S. (Liudmila S.); Bliss, B. (Brian); Yang, M. (Mingyu); Ochoa-Álvarez, I. (Idoia); Fostier, J. (Jan); Ostermann, J. (Jörn)
Motivation: In an effort to provide a response to the ever-expanding generation of genomic data, the International Organization for Standardization (ISO) is designing a new solution for the representation, compression and management of genomic sequencing data: the Moving Picture Experts Group (MPEG)-G standard. This paper discusses the first implementation of an MPEG-G compliant entropy codec: GABAC. GABAC combines proven coding technologies, such as context-adaptive binary arithmetic coding, binarization schemes and transformations, into a straightforward solution for the compression of sequencing data. Results: We demonstrate that GABAC outperforms well-established (entropy) codecs in a significant set of cases and thus can serve as an extension for existing genomic compression solutions, such as CRAM. Availability and implementation: The GABAC library is written in C++. We also provide a command line application which exercises all features provided by the library. GABAC can be downloaded from https://github.com/mitogen/gabac.