Read-Pair Sequence Assembly for Chromosome-Scale Contigs
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Solution Overview
Problem
Current high-throughput sequencing methods are inefficient and time-consuming for achieving long-range linkage and haplotype phasing, requiring computationally intensive assembly of nucleic acid sequences.
Innovation Solution
Methods and systems for scaffolding nucleic acid data using read pairs to infer phase and physical linkage, optimizing contig positioning and orientation to match expected read pair distance distributions, enabling efficient chromosome-scale contiguity assembly.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If computationally intensive assembly methods are used to achieve long-range linkage and haplotype phasing, then assembly accuracy is improved, but assembly time and computational resources increase significantly
Solution Approach 1:
The patent segments the assembly process into distinct phases: contig construction from reads, scaffolding using read-pair information, and gap filling. This segmentation allows each phase to be optimized independently, reducing overall computational complexity while maintaining accuracy
Solution Approach 2:
The patent performs preliminary actions by constructing contigs and identifying read-pair links before the main assembly process. Read-pair separation distributions are pre-calculated and used as constraints during scaffolding, reducing the computational burden during the actual assembly operation
2Quantity of substance
If traditional sequencing assembly methods are used, then comprehensive sequence coverage is achieved, but computational complexity and processing time increase
Solution Approach 1:
The patent introduces read-pair separation distribution as an intermediary constraint that mediates between raw sequencing data and final assembly. This intermediary structure organizes the data in a way that reduces computational complexity during the assembly process while maintaining comprehensive sequence coverage
Solution Approach 2:
The patent changes key parameters by using read-pair separation distances as a primary organizing principle rather than traditional overlap-based approaches. This parameter change simplifies the computational model while maintaining the ability to achieve comprehensive sequence coverage
Data Source
AI summary
Disclosed herein are compositions, systems and methods related to sequence assembly, such as nucleic acid sequence assembly of single reads and contigs into larger contigs and scaffolds through the use of read pair sequence information, such as read pair information indicative of nucleic acid sequence phase or physical linkage.