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A benchmark study of compression software for human short-read sequence data.

Raphael O Betschart1,2, Felix Thalén1, Stefan Blankenberg1,3,4,5

  • 1Cardio-CARE, Medizincampus Davos, Herman-Burchard-Str. 12, Davos Wolfgang, 7265, Davos, Switzerland.

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|May 2, 2025
PubMed
Summary
This summary is machine-generated.

Efficient data compression is vital for whole genome sequencing. Specialized tools like DRAGEN ORA and Genozip offer superior compression ratios for fastq.gz files compared to repaq and SPRING.

Keywords:
BAMCRAMDNA sequencingFASTQGVCFIllumina sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Data Science

Background:

  • Whole genome sequencing generates massive datasets, necessitating efficient data compression for storage and transfer.
  • Cost-effective management of genomic data is critical for large-scale research initiatives.

Purpose of the Study:

  • To benchmark the performance of specialized compression tools for paired-end fastq.gz files.
  • To compare Genozip's BAM file compression against SAMtools.
  • To evaluate compression ratios, speed, and file format compatibility.

Main Methods:

  • Benchmarking of DRAGEN ORA, Genozip, repaq, and SPRING on paired-end fastq.gz files from the genome-in-a-bottle consortium.
  • Comparative analysis of Genozip and SAMtools for BAM file compression.
  • Assessment of compression ratios, compression/decompression times, and file format support.

Main Results:

  • All tested tools provided lossless compression.
  • DRAGEN ORA and Genozip achieved compression ratios of approximately 1:6 for fastq.gz files.
  • Repaq and SPRING showed lower compression ratios (1:2 and 1:4, respectively) and longer processing times.
  • Genozip offered ~16% better compression for BAM files than SAMtools, though SAMtools produces widely compatible CRAM files.
  • Genozip supports multiple file formats, unlike ORA, repaq, and SPRING which are limited to fastq.gz.

Conclusions:

  • Specialized software effectively compresses paired-end short-read sequence data.
  • Commercial tools generally provide higher compression ratios than freely available options.
  • Genozip offers a balance of high compression, broad format support, and accessible source code, despite requiring a license.