Sequencing Quality Score Tier Encoding for Smaller Genomic Files
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Solution Overview
Problem
Current methods for compressing quality scores from nucleic acid sequencing data are inefficient, leading to large file sizes and slow compression speeds, which hinder data storage, transmission, and analysis.
Innovation Solution
The proposed method involves initial encoding of quality scores using base-x numbers and subsequent compression using techniques like Prediction by Partial Matching (PPMD) to reduce data size before processing by a compression engine, allowing for faster and more efficient compression.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional compression methods are used on quality scores, then the data can be compressed, but the file sizes remain large and compression speeds are slow
Solution Approach 1:
The patent segments the quality score data into distinct components: base call data and quality score data. It further segments quality scores into different quality tiers (e.g., high quality, medium quality, low quality). This segmentation allows for targeted compression strategies applied to different data types and quality levels, improving overall compression efficiency while maintaining data integrity.
Solution Approach 2:
The patent changes the representation parameters of quality scores by converting them from raw Phred scores to compressed formats. It applies parameter transformations such as rounding quality scores to nearest tiers, encoding them in reduced bit-depth formats, or mapping them to smaller integer ranges. These parameter changes significantly reduce the storage requirements while preserving the essential quality information needed for genomic analysis.
2Quantity of substance
If quality scores are compressed to reduce file size, then storage efficiency improves, but data precision may be compromised
Solution Approach 1:
The patent applies controlled parameter changes by transforming quality scores through defined mapping functions that preserve relative quality relationships. Quality scores are rounded to nearest standardized tiers or encoded in lossless compressed formats, ensuring that the compressed representation maintains the same discriminatory power as the original scores. This approach reduces file size while preserving measurement precision for downstream analysis.
Solution Approach 2:
The patent performs preliminary quality assessment and categorization before compression. By pre-identifying which quality scores fall into which quality tiers and applying appropriate compression schemes to each tier, the system ensures that precision is maintained where needed while maximizing compression where possible. This preliminary action prevents loss of critical quality information during the compression process.
Data Source
AI summary
Methods, systems, and computer programs for compressing nucleic acid sequence data. A method can include obtaining nucleic acid sequence data representing: (i) a read sequence, and (ii) a plurality of quality scores, determining whether the read sequence includes at least one “N” base, based on a determination that the read sequence does not include at least one “N” base, generating a first encoded data set by using a first encoding process to encode each of the quality scores of the read sequence using a base-(x minus 1) number, where x is an integer representing a number of different quality scores used by the nucleic acid sequencing device, and using a second encoding process to encode the first encoded data set, thereby compressing the data to be compressed.