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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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JARVIS3: an efficient encoder for genomic data.

Maria J P Sousa1,2,3, Armando J Pinho1,2,3, Diogo Pratas1,2,3,4

  • 1Institute of Electronics and Informatics Engineering of Aveiro (IEETA), University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.

Bioinformatics (Oxford, England)
|December 14, 2024
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Summary
This summary is machine-generated.

JARVIS3 offers efficient reference-free compression for genomic sequences, significantly improving computational speed and reducing storage needs. This open-source tool enhances genomic data analysis and management.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomic Data Science

Background:

  • Large-scale genomic projects face challenges in managing storage space, energy consumption, and costs.
  • Efficient compression of genomic sequences is crucial for reducing the environmental footprint of data storage.

Purpose of the Study:

  • To introduce JARVIS3, an advanced tool for efficient reference-free compression of genomic sequences.
  • To enhance computational efficiency and compression ratios for genomic data.

Main Methods:

  • Development of JARVIS3 using C programming language, building on JARVIS2.
  • Implementation of enhanced table memory models and probabilistic lookup-tables in repeat models.
  • Offering three distinct profiles for varying computation speed and compression ratios.

Main Results:

  • JARVIS3 demonstrates substantial speed improvements over JARVIS2 with slightly better compression.
  • The tool supports FASTA and FASTQ data formats with parallel computation capabilities.
  • Includes modes for bit information output and Normalized Compression/bit rates for analysis.

Conclusions:

  • JARVIS3 provides an open-source solution for efficient genomic data compression and analysis.
  • The tool offers flexibility through multiple compression profiles and parallel processing.
  • JARVIS3 contributes to reducing the storage burden and environmental impact of large genomic datasets.