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RENANO: a REference-based compressor for NANOpore FASTQ files.

Guillermo Dufort Y Álvarez1, Gadiel Seroussi1, Pablo Smircich2,3

  • 1Facultad de Ingeniería, Universidad de la República, Montevideo, 11300, Uruguay.

Bioinformatics (Oxford, England)
|June 15, 2021
PubMed
Summary
This summary is machine-generated.

New data compression software, RENANO, efficiently compresses large nanopore sequencing FASTQ files. It offers significant improvements over existing methods, reducing data transmission and storage costs for genomic data.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Data Compression

Background:

  • Nanopore sequencing generates massive genomic datasets (up to 8.5 TB in <72 hours).
  • Efficient compression methods are crucial for managing the costs of transmitting and storing this data.

Purpose of the Study:

  • Introduce RENANO, a novel reference-based lossless compressor for nanopore FASTQ files.
  • Enhance base call sequence compression compared to the state-of-the-art ENANO.

Main Methods:

  • Developed two compression algorithms for RENANO based on reference genome availability (shared or compressor-side only).
  • Evaluated RENANO's performance against ENANO and Genozip using public nanopore datasets.

Main Results:

  • RENANO improved base call sequence compression by 39.8% (scenario 1) and 33.5% (scenario 2) over ENANO.
  • Overall file compression improvements averaged 12.7% (scenario 1) and 10.6% (scenario 2).
  • RENANO outperformed the general-purpose genomic compressor Genozip.

Conclusions:

  • RENANO offers superior compression for nanopore sequencing data.
  • The software is freely available, facilitating its adoption in genomic research.