ArticleBioinformatics (Oxford, England)2024
JARVIS3: an efficient encoder for genomic data.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- FFC: a scalable FASTA compressor.Bioinformatics (Oxford, England) · 2026Article
- Environmental considerations in human genomic data governance: overcoming normative challenges.BMC medical ethics · 2026Article
- MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.GigaScience · 2026Article
- Evaluation of sequencing reads at scale using rdeval.Bioinformatics (Oxford, England) · 2025Article
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Authors and funding
3 authors.
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Abstract
motivationLarge-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.
resultsWe 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.