Details
| Originalsprache | Englisch |
|---|---|
| Seiten (von - bis) | 2275-2277 |
| Seitenumfang | 3 |
| Fachzeitschrift | BIOINFORMATICS |
| Jahrgang | 36 |
| Ausgabenummer | 7 |
| Frühes Online-Datum | 12 Dez. 2019 |
| Publikationsstatus | Veröffentlicht - 1 Apr. 2020 |
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.
ASJC Scopus Sachgebiete
- Mathematik (insg.)
- Statistik und Wahrscheinlichkeit
- Biochemie, Genetik und Molekularbiologie (insg.)
- Biochemie
- Biochemie, Genetik und Molekularbiologie (insg.)
- Molekularbiologie
- Informatik (insg.)
- Angewandte Informatik
- Informatik (insg.)
- Theoretische Informatik und Mathematik
- Mathematik (insg.)
- Computational Mathematics
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in: BIOINFORMATICS, Jahrgang 36, Nr. 7, 01.04.2020, S. 2275-2277.
Publikation: Beitrag in Fachzeitschrift › Artikel › Forschung › Peer-Review
}
TY - JOUR
T1 - GABAC
T2 - An arithmetic coding solution for genomic data
AU - Voges, Jan
AU - Paridaens, Tom
AU - Müntefering, Fabian
AU - Mainzer, Liudmila S.
AU - Bliss, Brian
AU - Yang, Mingyu
AU - Ochoa, Idoia
AU - Fostier, Jan
AU - Ostermann, Jörn
AU - Hernaez, Mikel
N1 - Funding information: This work has been partially supported by grants 2018-182798 and 2018-182799 from the Chan Zuckerberg Initiative DAF, a donor advised fund of the Silicon Valley Community Foundation, a Strategic Research Initiative from UIUC and the Mayo Clinic Center for Individualized Medicine, and the Todd and Karen Wanek Program for Hypoplastic Left Heart Syndrome. This work was a part of the Mayo Clinic and Illinois Strategic Alliance for Technology-Based Healthcare.
PY - 2020/4/1
Y1 - 2020/4/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85083073632&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btz922
DO - 10.1093/bioinformatics/btz922
M3 - Article
C2 - 31830243
AN - SCOPUS:85083073632
VL - 36
SP - 2275
EP - 2277
JO - BIOINFORMATICS
JF - BIOINFORMATICS
SN - 1367-4803
IS - 7
ER -