4 results about "Contig" patented technology

A method and system for virus detection in tumor RNA sequencing data are disclosed. The method includes preprocessing the raw tumor RNA sequencing data; inputting the processed tumor RNA sequencing data into sequence-information-based channels and codon-based channels for feature extraction to generate a feature matrix; constructing a sequence information prediction model and a codon information prediction model, and inputting the feature matrices generated from the sequence information-based channels and codon-based channels into the sequence information prediction model and codon information prediction model, respectively, for training and optimization; predicting the virus probability of each sequencing read to obtain a model score; and selecting viral sequencing reads based on the model scores to assemble viral contigs. This invention improves the accuracy and robustness of virus monitoring by introducing a multimodal deep learning method, and can adaptively process sequencing data from different sources and of different lengths, thereby better meeting the needs of medical and research fields for virus identification in tumor sequencing data.

This application provides a method and apparatus for identifying HPV integration into newly formed chromatin loops, relating to the field of bioinformatics. The method includes: acquiring interaction sequencing read data and determining HPV reference sequences and host reference sequences; identifying HPV integration breakpoints based on chimeric read characteristics, split read characteristics, and abnormal pairing end characteristics; constructing fusion contigs based on breakpoint directions to obtain a breakpoint-aware extended reference set; comparing the interaction sequencing read data with the breakpoint-aware extended reference set, and obtaining high-confidence cross-genomic anchor pairs based on breakpoint-aware alignment constraints; clustering the anchor pairs and screening target HPV-loops; calculating the newborn score of the target HPV-loop and outputting the chromatin loop identification result. This application solves the problem of low accuracy and identification bias that often occurs in traditional interaction localization systems during the identification of newly formed chromatin loops.

The application discloses an aspergillus telomere-to-telomere genome assembly method, device, equipment and storage medium. The method comprises the following steps: using a plurality of sequencing sequence assembly tools to assemble target aspergillus long read genome sequencing data from scratch to obtain a first assembled genome; selecting a first assembled genome meeting a preset condition as an initial assembled genome; integrating other first assembled genomes to fill gaps between repeat regions of the initial assembled genome to obtain a second assembled genome; aligning the long read genome sequencing data to the second assembled genome, identifying abnormal coverage regions and correcting sequences to obtain a third assembled genome; aligning a reference genome to the third assembled genome, connecting and orienting different contigs, and mounting the contigs to chromosomes to obtain a fourth assembled genome; and aligning the long read genome sequencing data and short read sequencing data to the fourth assembled genome for correction to obtain an aspergillus telomere-to-telomere genome assembly result.

This invention discloses a chromosome-level gapless genome assembly system and method based on a multi-layer computational graph, belonging to the field of bioinformatics. The system includes a data preprocessing module, a multi-layer computational graph construction module, an inter-layer communication module, a pathfinding module, a sequence generation module, and a quality assessment module. The multi-layer computational graph structure comprises four layers: a first-layer sequence overlap graph handles read-level overlap relationships; a second-layer fragment connection graph handles contig-level connection relationships; a third-layer scaffold construction graph utilizes Hi-C data for chromosome-level assembly; and a fourth-layer gap-filling graph employs differentiated filling strategies for different types of gaps. The inter-layer communication module enables bidirectional information transfer and conflict resolution. This invention achieves true chromosome-level gapless genome assembly, improving assembly continuity by 3-5 times and reducing the number of gaps by more than 90%.