Quality Score Encoding for Faster Sequencing 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 method involves initial encoding of quality scores using base-x numbers and subsequent encoding processes, such as Prediction by Partial Matching (PPMD) implementation of a range encoder, to reduce data size before compression, allowing for 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 applies preliminary encoding actions before compression by converting quality scores into base-x number representations. This pre-processing step transforms the original quality score data into a more compact form that subsequent compression algorithms can process more efficiently, thereby improving both compression speed and compression ratio.
Solution Approach 2:
The patent changes the parameter representation of quality scores by converting them from their original format to base-x number systems. This parameter transformation reduces the data size and alters the data structure to be more amenable to compression, directly addressing the issue of low compression ratios and slow compression speeds.
2Quantity of substance
If quality scores are not pre-encoded, then compression can be performed directly, but the input data size remains large reducing compression efficiency
Solution Approach 1:
The patent performs preliminary encoding of quality scores into base-x representations before the compression process. This pre-action reduces the input data size by transforming the quality score information into a more compact format, which then feeds into the compression algorithm with reduced data volume, improving overall compression efficiency.
Solution Approach 2:
The patent segments the quality score data by dividing it into base-x number representations. This segmentation breaks down the original large-quality-score dataset into smaller, more manageable units that can be processed more efficiently by compression algorithms, thereby reducing input data size and improving compression efficiency.
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.