Genome Scaffold Construction Using Paired-End Read Gap Estimation
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Solution Overview
Problem
Current methods for constructing genome scaffolds are inefficient with short sequencing reads, leading to low precision and inability to effectively assemble sequencing fragments, especially with Second-Generation Sequencing Methods like Solexa, Solid, and 454.
Innovation Solution
A computer-implemented method involving mapping double-barreled sequencing data to contigs, calculating gap sizes, constructing scaffolds based on these gaps and orientations, detecting and masking repeat contigs, linearizing the scaffold, and recalculating gap sizes to improve precision and accuracy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If current construction method links sequencing fragments with overlaps to build scaffold, then the method can assemble fragments, but the precision is low due to short overlaps from Second-Generation Sequencing Method
Solution Approach 1:
The patent introduces paired-end sequencing reads as an intermediary element that spans across contigs and gaps. These reads serve as mediators to establish relationships between contigs separated by gaps, enabling precise gap size estimation and contig ordering without relying on long overlaps. The paired-end reads bridge the gap between assembled contigs, providing indirect evidence for scaffold construction.
Solution Approach 2:
The patent transitions from one-dimensional overlap-based assembly to a two-dimensional approach by utilizing paired-end read information that provides both positional and distance information. The insert size distribution from paired-end reads adds a new dimension of information (distance estimation) that complements the traditional overlap-based contig assembly, enabling more accurate scaffold construction.
2Productivity
If short sequencing reads are used from Second-Generation Sequencing Method, then throughput is high and cost is low, but the ability to assemble sequencing fragments into scaffold is insufficient
Solution Approach 1:
The patent segments the genome assembly process into distinct phases: contig assembly using overlap information, and scaffold construction using paired-end read information. This segmentation allows each phase to use the most appropriate data type - short reads for contig assembly and paired-end reads for scaffold construction - thereby maintaining high throughput while improving assembly reliability.
Solution Approach 2:
The patent changes the parameters used for assembly by utilizing insert size distribution from paired-end reads as a new parameter for gap size estimation. Instead of relying solely on read length and overlap parameters, the method incorporates statistical parameters from paired-end sequencing (insert size, standard deviation) to improve scaffold assembly reliability while maintaining the advantages of short-read sequencing.
3Loss of information
If repeat contigs are present in scaffold, then the scaffold contains complete information, but the assembly becomes ambiguous and difficult to linearize
Solution Approach 1:
The patent performs preliminary identification and masking of repeat contigs before the final scaffold linearization step. By detecting repeat regions early in the process and masking them temporarily, the method prevents these complex regions from interfering with the linearization algorithm, while still preserving the underlying paired-end read information for later recovery and resolution.
Solution Approach 2:
The patent extracts and separates repeat contig information from the rest of the scaffold construction process. Repeat contigs are identified, masked, and handled separately from unique contigs, allowing the main scaffold assembly to proceed without ambiguity while repeat regions are resolved through alternative methods using paired-end read information.
Data Source
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AI summary
The present invention relates to gene engineering filed, and provides a genome sequencing device, construction method of fragments assembling scaffold and system thereof. The method comprises the following steps: mapping the double-barreled data obtained through sequencing to contigs; calculating the mean length between contigs based on multiple pairs of double-barreled data mapped to contigs, which is taken as the gap size between contigs; constructing scaffold based on gap size between contig and the double-barreled relation between contigs; and obtaining complete scaffold graph. Since the mean length between contigs is calculated from multiple pairs of double-barreled data and is taken as the gap size between contigs, the estimation precision of gap size between contigs is improved greatly. It can be used for genome sequencing including short sequencing read length to finish task of assembling sequencing fragments.