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Updated: Sep 3, 2025

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans
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CMIC: an efficient quality score compressor with random access functionality.

Hansen Chen1, Jianhua Chen2, Zhiwen Lu1

  • 1School of Information, Yunnan University, Chenggong Campus, Kunming, Yunnan, China.

BMC Bioinformatics
|July 23, 2022
PubMed
Summary
This summary is machine-generated.

A new lossless compressor, CMIC, efficiently compresses FASTQ quality scores, offering high compression rates and fast speeds. This method uniquely supports random access, improving genomic data management.

Keywords:
FASTQLossless compressorQuality scoreRandom access

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Area of Science:

  • Bioinformatics
  • Genomic Data Compression

Background:

  • Genome sequencing costs have decreased, leading to exponential growth in genomic data.
  • Efficient compression of FASTQ quality scores is crucial for managing large datasets.
  • Existing quality score compression methods often lack random access support.

Purpose of the Study:

  • To develop a lossless quality score compressor with high compression rate, speed, and random access capability.
  • To address the limitations of current quality score compression techniques.

Main Methods:

  • Proposed CMIC (Classification, Mapping, Indexing, Compression), an adaptive compressor for quality score sequences.
  • Implemented a four-part framework: classification, mapping, indexing, and compression.

Main Results:

  • CMIC achieved high compression rates, reducing file sizes by up to 21.91% compared to LCQS.
  • Demonstrated superior compression and decompression speeds over other compressors in most cases.
  • Provided faster random access speeds than LCQS for compressed quality scores.

Conclusions:

  • CMIC offers excellent performance in compression rate, speed, and random access for quality score sequences.
  • The developed compressor is specifically designed for efficient handling of genomic data.
  • CMIC is available via a public GitHub repository.