GABAC: an arithmetic coding solution for genomic data

Abstract

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.

Fig. 1.

Rank of compression performance (L) and speed (R). Dots were jittered for clarity. The x-axes show the test set ID (01 and 02) from which the descriptor stream files were generated. The y-axes denote the actual ranks. Each dot depicts the ranking a codec achieved on one specific descriptor stream file. The red lines denote the mean ranks, averaged over both test items. (Color version of this figure is available at Bioinformatics online.)