GABAC: an arithmetic coding solution for genomic data
Jan Voges 1 , Tom Paridaens 2 , Fabian Müntefering 1 , Liudmila S Mainzer 3 4 , Brian Bliss 3 , Mingyu Yang 5 , Idoia Ochoa 5 , Jan Fostier 2 , Jörn Ostermann 1 , Mikel Hernaez 4
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.
Supplementary information: Supplementary data are available at Bioinformatics online.
CITA DEL ARTÍCULO Bioinformatics. 2020 Apr 1;36(7):2275-2277. doi: 10.1093/bioinformatics/btz922