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GeneComp, a new reference-based compressor for SAM files.

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GeneComp offers a new way to compress genomic data (SAM files), reducing file sizes significantly. This new method achieves better compression ratios than existing algorithms, even in lossless mode.

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Area of Science:

  • Bioinformatics
  • Genomic Data Analysis
  • Data Compression

Background:

  • Advancements in DNA sequencing generate massive genomic datasets.
  • The Sequence Alignment Map (SAM) format is standard for genomic data, but files are very large (terabytes).
  • Efficient storage and processing of SAM files require effective compression techniques.

Purpose of the Study:

  • To introduce GeneComp, a novel reference-based compressor for SAM files.
  • To provide users with adjustable compression levels tailored to their specific needs.
  • To explore lossy compression of quality scores within SAM files to improve compression ratios.

Main Methods:

  • Development of a new reference-based compression algorithm, GeneComp.
  • Implementation of adjustable compression levels for user-defined needs.
  • Inclusion of a lossy compression option for quality scores, a major component of SAM file size.

Main Results:

  • GeneComp achieves superior compression ratios compared to existing algorithms in lossless mode.
  • The proposed compressor demonstrates effectiveness in handling large genomic datasets.
  • Lossy compression of quality scores significantly contributes to overall file size reduction.

Conclusions:

  • GeneComp provides an effective solution for compressing large SAM files.
  • The algorithm offers flexibility through adjustable compression levels and lossy quality score compression.
  • GeneComp represents an advancement in genomic data compression, outperforming previous methods.