An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values

Area of Science:

• Bioinformatics
• Genomics
• Data Compression

Background:

• Lossy compression of genomic data, particularly quality values, is under consideration for standardization.
• Evaluating the impact of such compression on downstream analyses like variant calling is crucial.
• Existing methods lack a standardized framework for rigorous comparison.

Purpose of the Study:

• To specify and validate an evaluation framework for lossy compressors of genome sequencing quality values.
• To establish reference data, test sets, tools, and metrics for this evaluation.
• To assess the effect of quality value compression on human genome variant calling.

Main Methods:

• Development of a comprehensive evaluation framework.
• Definition of standardized reference datasets and test cases.
• Selection of appropriate metrics to quantify compression impact.
• Validation using two state-of-the-art genomic compressors.

Main Results:

• The proposed framework provides a standardized approach for comparing lossy quality value compressors.
• Initial validation demonstrates the framework's capability to assess compression effects on variant calling.
• The framework is designed to support ongoing standardization efforts.

Conclusions:

• A robust evaluation framework is essential for assessing lossy compression of genome sequencing quality values.
• This framework facilitates objective comparisons and informs standardization activities.
• The validation confirms its utility in understanding the impact on human genome variant calling.