Quality Score Encoding for Faster Genomic Data Compression
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Solution Overview
Problem
Current methods for compressing quality scores from nucleic acid sequencing data are inefficient, leading to slower compression speeds and lower compression ratios, which result in larger file sizes and increased storage and transmission costs.
Innovation Solution
The proposed solution involves a multi-stage compression method that initially encodes quality scores using base-x encoding, where x is an integer representing the number of unique quality scores, followed by further encoding using techniques like Prediction by Partial Matching (PPMD) to reduce the data size before inputting it into a compression engine, thereby achieving faster compression speeds and higher compression ratios.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If current compression methods are used for quality scores, then compression is performed, but compression speed is slow and compression ratio is low
Solution Approach 1:
The patent segments the compression process into multiple distinct stages: base-x encoding stage, PPMD encoding stage, and final compression stage. Each stage processes the quality score data with a specific algorithm optimized for that phase, allowing parallel processing and reducing the computational bottleneck that limits compression speed in single-stage methods.
Solution Approach 2:
The patent applies preliminary encoding actions before the main compression process. Base-x encoding is performed first to convert quality scores into a compact representation, and PPMD encoding is applied subsequently to further reduce data size. These preliminary encoding steps prepare the data in an optimal format for the final compression stage, significantly improving both speed and ratio.
2Quantity of substance
If current compression methods are used for quality scores, then compression is performed, but compression ratio is low resulting in larger file sizes
Solution Approach 1:
The patent changes the parameter representation of quality scores through base-x encoding, where x varies based on the range of quality score values. This parameter transformation reduces the average number of bits required to represent each quality score. Subsequent PPMD encoding further transforms the parameters by identifying and exploiting statistical patterns in the encoded data, achieving higher compression ratios.
Solution Approach 2:
The patent introduces intermediate encoding steps between the original quality scores and the final compressed output. Base-x encoding acts as an intermediary that converts quality scores into a more compact form, and PPMD encoding serves as a second intermediary that further compresses this intermediate representation. These intermediary transformations enable the final compression stage to achieve superior compression ratios compared to direct compression of raw quality scores.
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 includes at least one “N” base, generating, by one or more computers, a first encoding data set by using a first encoding process to encode each set of four quality scores of the read sequence into a single byte of memory, and using a second encoding process to encode the first encoded data set, thereby compressing the data to be compressed.