JARVIS3: an efficient encoder for genomic data.

ABSTRACT:

Motivation

Large-scale genomic projects grapple with the complex challenge of reducing medium- and long-term storage space and its associated energy consumption, monetary costs, and environmental footprint.

Results

We present JARVIS3, an advanced tool engineered for the efficient reference-free compression of genomic sequences. JARVIS3 introduces a pioneering approach, specifically through enhanced table memory models and probabilistic lookup-tables applied in repeat models. These optimizations are pivotal in substantially enhancing computational efficiency. JARVIS3 offers three distinct profiles: (i) rapid computation with moderate compression, (ii) a balanced trade-off between time and compression, and (iii) slower computation with significantly higher compression ratios.

SUBMITTER: Sousa MJP 

PROVIDER: S-EPMC11645547 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature