Paired Nucleic Acid Sequence Alignment Quality Assessment
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Solution Overview
Problem
Conventional nucleic acid sequencing tools inaccurately estimate alignment quality due to their inability to differentiate between read fragment types, such as single, mate-pair, and paired-end reads, which affects the reliability of sequence assembly and analysis.
Innovation Solution
A computer-implemented method and system for classifying and determining the quality of alignments of paired nucleic acid sequence reads by calculating a pairing quality value (PQV) based on the distance between tags and total mismatches, using a processor to interrogate sequencing data and output alignments with associated quality values.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional mapping tools are used to align sequence reads, then alignment can be performed, but alignment quality estimation is inaccurate
Solution Approach 1:
The patent applies local quality by differentiating alignment quality assessment based on read fragment types (single, mate-pair, paired-end). Instead of using a uniform quality estimation method for all reads, the system calculates separate pairing quality values (PQV) for different read configurations, allowing each local type to receive appropriate quality assessment tailored to its specific characteristics and error profiles.
2Adaptability or versatility
If conventional mapping tools are used, then alignment can be performed, but quality values cannot differentiate between read fragment types
Solution Approach 1:
The patent segments the quality value determination process into separate components for different read fragment types. It calculates base quality values for individual reads and pairing quality values for read pairs, then combines them differently depending on whether the reads are singletons, mate-pairs, or paired-end reads. This segmentation allows precise quality assessment for each read type while maintaining overall system versatility.
Data Source
AI summary
A computer-implemented method for classifying alignments of paired nucleic acid sequence reads is disclosed. A plurality of paired nucleic acid sequence reads is received, wherein each read is comprised of a first tag and a second tag separated by an insert region. Potential alignments for the first and second tags of each read to a reference sequence is determined, wherein the potential alignments satisfies a minimum threshold mismatch constraint. Potential paired alignments of the first and second tags of each read are identified, wherein a distance between the first and second tags of each potential paired alignment is within an estimated insert size range. An alignment score is calculated for each potential paired alignment based on a distance between the first and second tags and a total number of mismatches for each tag.