JARVIS3: an efficient encoder for genomic data

• DOI: 10.1093/bioinformatics/btae725
• Publication Date: 2024-12-14T11:53:59Z
• Authors: Maria J P Sousa; Armando J Pinho; Diogo Pratas
• Keywords: Applications Note; Genetics, developmental biology, physiology; 0206 medical engineering; Medical biotechnology; Compression; 02 engineering and technology

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. The implementation of JARVIS3 is rooted in the C programming language, building upon the success of its predecessor, JARVIS2. JARVIS3 shows substantial speed improvements relative to JARVIS2 while providing slightly better compression. Furthermore, we provide a versatile C/Bash implementation, facilitating the application in FASTA and FASTQ data, including the capability for parallel computation. In addition, JARVIS3 includes a mode for outputting bit information, as well as providing the Normalized Compression and bit rates, facilitating compression-based analysis. This establishes JARVIS3 as an open-source solution for genomic data compression and analysis.

Availability and implementation JARVIS3 is freely available at https://github.com/cobilab/jarvis3.