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FaStore: a space-saving solution for raw sequencing data.

Lukasz Roguski1,2, Idoia Ochoa3, Mikel Hernaez4

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Summary
This summary is machine-generated.

FaStore is a new compressor for FASTQ files that significantly improves data compression. Its lossy modes offer substantial gains while preserving essential genomic information for variant calling.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Data Compression

Background:

  • The increasing affordability of DNA sequencing generates massive amounts of raw sequencing data.
  • Storing, processing, and transmitting these large datasets present significant computational challenges.
  • Efficient data compression is crucial for managing the growing volume of genomic information.

Purpose of the Study:

  • To introduce FaStore, a specialized compressor for FASTQ files.
  • To evaluate FaStore's compression performance in both lossless and lossy modes.
  • To assess the impact of FaStore's lossy compression on variant calling accuracy.

Main Methods:

  • FaStore employs a novel compression approach for FASTQ files, independent of reference sequences.
  • The study implemented and tested FaStore in lossless mode against existing algorithms.
  • Various lossy compression modes were analyzed for their effect on downstream variant calling.

Main Results:

  • FaStore in lossless mode demonstrated superior compression ratios compared to previous methods.
  • Lossy compression modes in FaStore achieved significant file size reductions.
  • Variant calling performance remained unaffected even with lossy compression, preserving critical genomic data.

Conclusions:

  • FaStore offers an effective solution for compressing large volumes of FASTQ data.
  • Lossy compression with FaStore provides substantial benefits without compromising essential genomic information for variant analysis.
  • FaStore is a valuable tool for precision medicine and genomic data management.