GABAC: an arithmetic coding solution for genomic data.
Bioinformatics
; 36(7): 2275-2277, 2020 04 01.
Article
em En
| MEDLINE
| ID: mdl-31830243
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.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Compressão de Dados
/
Sequenciamento de Nucleotídeos em Larga Escala
Idioma:
En
Ano de publicação:
2020
Tipo de documento:
Article