36 results about "Short read" patented technology

The invention discloses a reference-level high-quality genome assembly method, which is characterized in that a compPoFi tool integrates a plurality of high-performance assembly tools, does not need expensive ONT sequencing, and can realize multi-species reference-level high-quality genome assembly only by adopting a second-generation Illumina short read length, a third-generation HiFi (Revio platform, average read length of 25kb) and Hi-C chromatin conformation capture sequencing. The sequencing cost is obviously reduced. In order to solve the problem of genome assembly with a high transposition element ratio, the average read length of a HiFi sequencing library is required to reach 25kb so as to cross most transposition elements. Under the standard, a developed compPoFi tool is utilized, the assembly of the high-quality chromosome scale reference genome of the field worst weed beckmannia syzigachne is completed for the first time, all telomere and centromere regions are identified, and the 2.8 G beckmannia syzigachne genome is assembled to the near telomere to telomere (T2T) level. The invention provides a more economical high-quality genome assembly scheme, and lays a research foundation for understanding rapid adaptation and evolution of weeds under environmental stress.

The invention relates to the technical field of information, and discloses a method for carrying out automatic analysis and typing on HLA based on third-generation sequencing. The method comprises the steps that firstly, the HLA type of first sequencing read data of different data types of a to-be-detected sample is preliminarily judged, then second sequencing read data is selected, then the identified second sequencing read data of different HLA types and a corresponding HLA reference sequence are compared, verified and screened, and therefore the HLA type existing in the to-be-detected sample is determined; according to the method, long read length data generated based on a third-generation sequencing technology can be effectively processed, the calculation amount of accurate comparison is reduced, accurate analysis and report generation of typical third-generation HLA data within 15 minutes can be achieved, and the requirement for rapid HLA detection analysis is met; meanwhile, the method can be used for analyzing short read length data obtained by next-generation sequencing, and has relatively good data compatibility.

The invention relates to a method for identifying contaminating bacteria in a microbial sequencing sample based on single nucleotide polymorphism. Comprising the following steps: S1, obtaining a compared BAM file through BWA comparison software, and sorting the BAM file; s2, on the basis of the BAM file, outputting comparison information of each sequencing short read segment on each site on the reference genome, and extracting SNP and InDel information existing in each short read segment sequence; step S3, calculating an SNP similarity index and an SNP dissimilarity index; s4, taking the similarity and the dissimilarity as core input features of a RandomForest classification algorithm in machine learning, and establishing a three-classifier model; s5, quantitatively evaluating the richness of the planting bacteria in the polluted planting mixed bacteria; and S6, carrying out confidence scoring on a model judgment result. The invention provides a more accurate method for distinguishing a pollution sequence and a real colonization sequence in a sample, and can effectively estimate the abundance of microorganisms which may be both pollution bacteria and colonization bacteria.

The present application relates to the technical field of bioinformatics, in particular to a method for detecting microbial structural variation, mutation and insertion deletion based on second-generation sequencing. The present application is based on the short read Illumina second-generation sequencing strategy, through testing, using the current mainstream biological tools and combining the self-developed program, the automatic analysis of microbial metagenome structural variation (SV), single nucleotide variation (SNV / mutation) and small fragment insertion deletion (Indel) is realized, and the problems of low sensitivity, high false positive rate and low efficiency in the prior art for detecting variation under the metagenome background are significantly solved.

In accordance with embodiments, a processing unit receives a count table and an occurrence table for a reference sequence generated using a Burrows Wheeler Transform (BWT) algorithm. The reference sequence comprises a sequence of base pairs (bps). The processing unit stores a first part of the occurrence table in a first type of memory. The size of the first part of the occurrence table is determined based on a size of the first type of memory and a first number of bps of short reads (SRs) to be processed using the first type of memory. The processing unit receives a short read (SR) of a sample sequence. The SR comprises the first number of bps and a second number of bps. The processing unit performs alignment of the short read (SR) against the reference sequence using the count table and the occurrence table.

The application discloses a method for identifying large fragment sequence insertion of a target genomic region and application thereof, and belongs to the technical field of bioinformatics. In view of the problem that large fragment insertion variation is difficult to be accurately recognized in clinical metagenomic sequencing due to short sequencing read length, insufficient coverage and other factors, the application proposes to construct a reference sequence which can represent the insertion variation by means of manual construction, and to realize efficient identification of the insertion event of the target genomic region by combining a short read-based fast alignment process. The method overcomes the dependence of existing structural variation detection tools on high sequencing depth and long read length, has the advantages of fast identification speed, high sensitivity and high accuracy, and is suitable for rapid screening of large fragment insertion related to drug resistance mechanism in clinical samples. Meanwhile, the method can be popularized for insertion variation analysis of other pathogen drug resistance related genes or genomic regions, and has a good clinical application prospect.

The invention discloses a haplotype horizontal transposon insertion identification method and system based on physical typing, and the method comprises the following steps: respectively comparing sequencing data to two sets of haplotype genomes, and obtaining a comparison score and a mismatch number after the sequencing data is compared to the two sets of haplotype genomes; for single-ended long-read-length sequencing data, a sequencing sequence is distributed to a haplotype with a higher comparison score; for double-end short read length sequencing data, adding the comparison score and the mismatching number of the double-end short read length to serve as the comparison score and the mismatching number of each pair of sequences, and distributing the sequencing sequences to haplotypes with higher comparison scores; and based on a physical typing result, separating out a comparison file of two haplotype genomes, and based on the comparison file, carrying out transposon insertion identification at a haplotype level. According to the method, transposon insertion identification is carried out on the haplotype level, the insertion difference of the transposon in the two haplotypes can be distinguished more clearly, and the identification resolution is improved.

Some embodiments of the methods and compositions provided herein relate to obtaining long read information from short reads of a target nucleic acid. Some embodiments include steps to selectively generate, mark, and amplify long nucleic acid fragments. Some embodiments include enriching for certain sequences in the long fragments with selection probes directed to certain challenging medically relevant genes (CMRG). Some embodiments also include fragmenting the long nucleic acid fragments into shorter fragments for sequencing, and informatically reconstructing a sequence of the target nucleic acid.

The invention discloses a method for calculating the length of autosomal telomeres of a crowd. The method comprises the following steps: S1, acquiring three-generation sequencing gene long fragment data of different age groups of the crowd; s2, identifying a long fragment containing a telomere sequence; s3, comparing the long fragment data of the third-generation sequencing gene in the step S1 to a reference genome; s4, grouping in chromosome and sequence directions according to a comparison result; s5, identifying and extracting positions of telomere sequences in the same chromosome and direction; sequencing according to the front and back positions of the telomere sequence on the chromosome, and determining a minimum starting position and a maximum ending position; according to the method, the advantage of long reading length of third-generation sequencing is utilized, the whole telomere area can be directly crossed, deviation caused by reading length of second-generation sequencing is avoided, the measurement result is more accurate and reliable, the efficiency is high, and the cost is low.

The application discloses a coronavirus transcriptome identification and analysis method, which comprises the following steps: using bwa software to perform sequence alignment on coronavirus second-generation sequencing original fastq files obtained from a short read archive SRA and NCBI reference genomes, to generate BAM files; calling and filtering single nucleotide polymorphisms SNPs through bcftools, and annotating the SNPs by using a vcf-annotator; performing CIGAR string analysis and breakpoint identification operations on the BAM files, to perform sgRNA identification; generating an expression matrix from the sgRNA identification result and performing transcriptome analysis. The application further discloses a coronavirus transcriptome identification and analysis system, which comprises a storage and a processor; the storage is provided with a computer program, and when the computer program is executed by the processor, the method described above is realized. The coronavirus transcriptome identification and analysis method and system provide a new cognitive means for coronavirus biology, and provide valuable resources for the development of future treatment methods.

The present invention relates to the technical field of protein detection, and discloses a protein detection method based on an arrayed nanopore structure, comprising the following steps: Step 1, processing array grooves on a chip thin film; Step 2, connecting a temperature control element to the bottom of the chip thin film; Step 3, fixing a protein at the bottom of the array grooves; Step 4, covering a phospholipid layer on the surface of the chip thin film; Step 5, electrically driving the embedding of functional proteins. By adopting the above-mentioned protein detection method based on an arrayed nanopore structure, the relative distance between two functional proteins in the nanopore structure can be adjusted by controlling the thickness of the chip film and the processing depth of the grooves, effectively solving the problem of short read lengths caused by the nano-space limitation of the peptide chain. At the same time, the arrayed combined protein sensor can also achieve high-throughput detection of peptide chains, realizing stable, long-read-length, and highly accurate protein sequencing.

The application discloses a method for adenovirus whole genome sequencing, a primer group and a kit thereof, and belongs to the technical field of DNA detection.The method for adenovirus whole genome sequencing comprises the following steps: S1, first round amplification is carried out by using first round amplification primers with sequences shown in SEQ ID NO.1 to SEQ ID NO.93 in Table 1; and S2, second round amplification is carried out by using second round amplification primers with sequences shown in SEQ ID NO.94 to SEQ ID NO.285 in Table 2.The average length of data sequenced by the method is 0.8 kb, compared with short read length of a second-generation platform, the uniformity of adenovirus coverage can be greatly improved, meanwhile, the adenovirus types are comprehensively covered, and the method can be widely promoted.

The invention provides an ITK-SYK fusion gene detection kit and detection method based on ultra-high depth sequencing, the ITK-SYK fusion gene detection kit comprises a plurality of primers, the detection method uses obtained cf-RNA as a template to amplify a target sequence and build a library, the obtained library is sequenced, offline data is analyzed, and the detection result of the ITK-SYK fusion gene detection kit based on ultra-high depth sequencing is obtained. And calculating the relative proportion of the ITK-SYK fusion gene. According to the detection method, the limit of digital PCR is broken through, the designed amplified fragment is shorter, the detection sensitivity is further improved, an SE50-SE75 short read length mode is used during sequencing, ultrahigh sequencing depth is achieved under the condition of extremely small data volume, 10 <-6 > low-frequency fusion mutation can be detected, the time required by the overall experimental process is as short as 1 day, and the report period is greatly shortened. The method is high in specificity, high in sensitivity, simple, convenient and rapid to operate and rigorous and reliable in result, provides a reliable method for related research of ITK-SYK gene fusion diseases, and is a convenient and non-invasive detection technology.

Some embodiments of the methods and compositions provided herein relate to obtaining long read information from short reads of a target nucleic acid. Some embodiments include steps to selectively generate, mark, and amplify long nucleic acid fragments. Some embodiments include enriching for certain sequences in the long fragments with selection probes directed to major histocompatibility complex (MHC) genes. Some embodiments also include fragmenting the long nucleic acid fragments into shorter fragments for sequencing, and informatically reconstructing a sequence of the target nucleic acid.

The invention discloses a method for assembling IGHV short-read-length double-end sequencing data, and the method comprises the following steps: obtaining IGHV short-read-length double-end sequencing data, and analyzing through an immune repertoire to obtain target cell sequencing data; splitting the target cell sequencing data into double-end read length data based on a plurality of different forward primers; dividing the double-end read length data of the first forward primer into forward read length data and reverse read length data, and calculating a maximum common sequence of the forward read length data and the double-end read length data of the second forward primer; assembling the forward read length data and the double-end read length data of the second forward primer according to the maximum common sequence; and repeating to obtain a full-length sequence of the IGHV. The method for acquiring the full length of the IGHV based on dynamic planning assembly can adapt to immune repertoire data generated by short read length sequencing, so that rapid, accurate, low-cost and convenient IGHV mutation detection is realized.

The invention discloses a method for identifying large-fragment sequence insertion in a target genome region and application of the method, and belongs to the technical field of bioinformatics. In order to solve the problem that large-fragment insertion variation is difficult to accurately identify due to factors such as short sequencing reading length and insufficient coverage in clinical metagenome sequencing, the invention proposes that a reference sequence capable of representing the insertion variation is artificially constructed and is combined with a rapid comparison process based on short reads to realize efficient identification of an insertion event in a target genome region. The method overcomes the dependence of an existing structure variation detection tool on high sequencing depth and long reading length, has the advantages of high identification speed, high sensitivity, high accuracy and the like, and is suitable for rapid screening of large fragment insertion related to a drug resistance mechanism in a clinical sample; meanwhile, the method can be popularized and applied to insertion variation analysis of other pathogen drug resistance related genes or genome areas, and has a good clinical application prospect.

The invention discloses a linker fixed on a chip and a sequencing method of a sample library connected to the linker, and relates to the technical field of sequencing. The linker comprises a P5 linker sequence and a P7 linker sequence, the P5 linker sequence comprises a first identification base and a second identification base, the first identification base is located at the position of a T base, and the second identification base is located at the position of a C base; the P7 linker sequence comprises a third identification basic group, and the third identification basic group is located at the position of the G basic group. According to the scheme provided by the invention, a traditional sequencing mode is changed, tag sequencing of the first end and the second end of the nucleic acid fragment can be carried out firstly, and then sequencing of the target fragments of the first end and the second end of the nucleic acid fragment can be carried out; in addition, during mixed sequencing in different read length modes, the result output time of short read length sequencing samples can be shortened; a sequencing mode of sequencing and splitting at the same time can be supported, and meanwhile, multi-node batch analysis result output is supported.

The present disclosure describes methods, non-transitory computer-readable media, and systems that can generate genotype calls from a combined pipeline for processing nucleotide reads from multiple read types / sources for robust and accurate genotype calling. For example, the disclosed systems can train and / or utilize a genotype call integration machine learning model to generate predictions of genotype calls based on data associated with a first type of nucleotide read (e.g., short reads) and a second type of nucleotide read (e.g., long reads). As disclosed, the disclosed systems can determine sequencing metrics and utilize a genotype call integration machine learning model to generate predictions (e.g., genotype probabilities, variant call classifications) for generating output genotype calls based on the sequencing metrics. The disclosed systems can utilize multiple such genotype call integration machine learning models to generate genotype calls for different variants, such as SNPs (Single Nucleotide Polymorphisms) and indels, with the genotype call integration machine learning model generating different predictions for each variant.

The application discloses a haplotype level transposon insertion identification method and system based on physical typing, and the method comprises the following steps: respectively aligning sequencing data to two sets of haplotype genomes, obtaining alignment scores and mismatch numbers after the sequencing data are aligned to the two sets of haplotype genomes; for single-end long read sequencing data, distributing the sequencing sequence to a haplotype with a larger alignment score; for double-end short read sequencing data, adding the alignment scores and the mismatch numbers of the double-end short reads as the alignment score and the mismatch number of each pair of sequences, and distributing the sequencing sequence to a haplotype with a larger alignment score; based on the physical typing result, separating the alignment files of the two sets of haplotype genomes, and identifying the transposon insertion at the haplotype level based on the alignment files. The application identifies the transposon insertion at the haplotype level, can more clearly distinguish the insertion differences of the transposon in the two sets of haplotypes, and improves the resolution of identification.

The present application discloses a method and apparatus for correcting long read assembly results using short read sequences. The method of the present application includes a cutting step of splitting the long read assembly result with a fixed threshold to obtain the split long read assembly result; and subsequent steps of building a library for the long read assembly result, a comparison step, a matching step for the comparison result, a conversion and sorting step for the comparison result, a library building step for the comparison result, and an error correction step for the long read assembly result based on the split long read assembly result. Finally, the error correction results are merged to obtain the error-corrected long read assembly result. The method of the present application can perform error correction using small memory nodes, significantly reducing the memory peak value, solving the problem that error correction cannot be performed without large memory nodes, and reducing the error correction cost of long length assembly results. Moreover, when resources are sufficient, the error correction method and apparatus of the present application can also be executed in parallel, reducing the execution time and improving the error correction efficiency.

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.

The application discloses a kind of based on rice infected tissue transcriptome sequencing of SRBSDV Quantitative method of virus, comprising: 1) obtain the genome assembly and gene annotation file of SRBSDV virus, and the high-throughput transcriptome sequencing original data of rice virus infected tissue;2) construct SRBSDV virus genome index module;3) obtain the non-redundant length of each gene in SRBSDV virus genome annotation file;4) obtain high-quality transcriptome sequencing data;5) obtain the total number of short reads of each sample in step 4);6) obtain individual level BAM file;7) obtain the original expression of different genes in each sample Virus;8) obtain gene expression standardization function FPKB.The application can more accurately evaluate the infection level of virus by means of standardized bioinformatics analysis framework;And more virology information can be mined, the maximization of data utilization is realized, support is provided for virus research and prevention and control, and the accuracy of virus quantification is improved.

Some embodiments of the methods and compositions provided herein relate to obtaining long read information from short reads of a target nucleic acid. Some embodiments include steps to selectively generate, mark, and amplify long nucleic acid fragments. Some embodiments include enriching for certain sequences in the long fragments with selection probes directed to certain genes throughout the genome and expressed regions with low mappability. Some embodiments also include fragmenting the long nucleic acid fragments into shorter fragments for sequencing, and informatically reconstructing a sequence of the target nucleic acid.

The present invention provides methods of sequencing long chromosomal fragments using a short read sequencing method by using two separate transposase-based fragmentation steps.

Some embodiments of the methods and compositions provided herein relate to blocked substrates in which non-specific binding of nucleic acids to the substrate is reduced. Some embodiments include use of carrier nucleic acids. More embodiments include the use of beads contacted with an oligonucleotide, such as an oligonucleotide containing one or more phosphorothioate bonds. Such substrates are useful in methods for obtaining long-read information from short reads of a target nucleic acid.

The application discloses a method for strain-level classification of metagenomic data based on a pan-genome graph, which first captures the genomes of multiple strains of each species as a reference through the technology of the pan-genome graph, instead of using only the representative genome of each species as a reference, expands the strain diversity, and enhances the alignment accuracy of metagenomic sequencing reads and the estimation of composition at the strain level; then, by using the corresponding short read alignment tool Giraffe and the long read alignment tool GraphAligner in the alignment of NGS and TGS metagenomic data with the pan-genome graph, two types of data can be efficiently processed at the same time; finally, by further optimizing the path abundance of the species-level classification results based on the pan-genome graph, multi-species strain-level classification can be realized. The application can solve the technical problem that the strain-level classification capability is limited due to the strategy of a single reference genome in the prior art.

The application provides ciliate-specific primers, ciliate-specific long primers and kits suitable for amplicon sequencing technology and applications, and specifically belongs to the field of molecular biology detection and high-throughput gene sequencing technology.The ciliate-specific primers include a forward primer CS322F and a reverse primer CS819R;the ciliate-specific long primers suitable for amplicon sequencing include a forward long primer LCS322F and a reverse long primer LCS819R.The ciliate-specific primers have broad-spectrum generality for ciliophora, are suitable for a short read length high-throughput sequencing method, and can be used for comprehensively analyzing the diversity and ecological functions of a ciliate community.The application can realize accurate detection and efficient analysis of the ciliate community, and provides technical support for environmental monitoring, germplasm resource development and ecological assessment.

The application relates to the field of information technology and discloses a method for automatically analyzing and typing HLA based on third-generation sequencing; first, the HLA types of first sequencing read data of different data types of a to-be-tested sample are preliminarily judged, then second sequencing read data is selected, then the identified second sequencing read data of different HLA types is compared with corresponding HLA reference sequences for verification and screening, so that the HLA types existing in the to-be-tested sample are determined; the method can effectively process long read length data generated based on third-generation sequencing technology, reduces the calculation amount of accurate comparison, can realize accurate analysis and report generation of typical third-generation HLA data within 15 minutes, and meets the demand of rapid HLA detection and analysis; meanwhile, the method can also analyze short read length data obtained by second-generation sequencing, and has good data compatibility.

This invention relates to a composition and method for the detection of Tuberculosis drug resistance by multiplex small amplicon based, targeted Next-Gen sequencing (tNGS) using ribonucleotide bases in the primers. It also provides a bioinformatic data analysis tool, for the prediction of drug resistance / susceptibility towards anti- tuberculosis therapy drugs. The invention provides an efficient, cost-effective solution for identifying drug resistance / susceptibility right after tuberculosis diagnosis. In addition, a short read NGS platform with massive parallel sequencing, along with data analysis of this invention, offers high sensitivity and specificity for detection of drug resistance.