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    Methods for hybridization based hook ligation
    35.
    发明授权
    Methods for hybridization based hook ligation 有权

    公开(公告)号：US11091791B2

    公开(公告)日：2021-08-17

    申请号：US15903424

    申请日：2018-02-23

    Applicant: Complete Genomics, Inc.

    Inventor： Yuan Jiang ,  Radoje Drmanac

    IPC: C12Q1/68 ,  C12Q1/6806

    Abstract: Provided herein are compositions, methods, and kits for enriching for one or more nucleic acid sequences of interest in a sample. The methods include providing a circular ligase, one or more 5′ hook probes and/or one or more 3′ hook probes and contacting the sample comprising the nucleic acids with the circular ligase and one or more 5′ hook probes and/or one or more 3′ hook probes under conditions to allow the hook probes to selectively bind to the one or more nucleic acid sequences of interest, and under conditions to form one or more hook products, each hook product comprising the hook probes and the one or more nucleic acid sequences of interest.

    METHODS FOR IDENTIFYING NUCLEOTIDES IN TARGET SEQUENCES
    37.
    发明申请
    METHODS FOR IDENTIFYING NUCLEOTIDES IN TARGET SEQUENCES 审中-公开

    公开(公告)号：US20200318183A1

    公开(公告)日：2020-10-08

    申请号：US16882461

    申请日：2020-05-23

    Applicant: Complete Genomics, Inc.

    Inventor： Radoje Drmanac

    IPC: C12Q1/6874 ,  C12Q1/6876 ,  C12Q1/6869 ,  C12Q1/686

    Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.

    Long fragment de novo assembly using short reads
    38.
    发明授权
    Long fragment de novo assembly using short reads 有权

    公开(公告)号：US10726942B2

    公开(公告)日：2020-07-28

    申请号：US14467797

    申请日：2014-08-25

    Applicant: Complete Genomics, Inc.

    Inventor： Radoje Drmanac ,  Bahram Ghaffarzadeh Kermani

    IPC: G16B30/00 ,  G16B30/20

    Abstract: Techniques perform de novo assembly. The assembly can use labels that indicate origins of the nucleic acid molecules. For example, a representative set of labels identified from initial reads that overlap with a seed can be used. Mate pair information can be used. A sequence read that aligns to an end of a contig can lead to using the other sequence read of a mate pair, and the other sequence read can be used to determine which branch to use to extend, e.g., in an external cloud or helper contig. A kmer index can include labels indicating an origin of each of the nucleic acid molecules that include each kmer, memory addresses of the reads that correspond to each kmer in the index, and a position in each of the mate pairs that includes the kmer. Haploid seeds can also be determined using polymorphic loci identified in a population.

    Basecaller for DNA sequencing using machine learning
    40.
    发明授权
    Basecaller for DNA sequencing using machine learning 有权

    公开(公告)号：US10068053B2

    公开(公告)日：2018-09-04

    申请号：US14571022

    申请日：2014-12-15

    Applicant: Complete Genomics, Inc.

    Inventor： Bahram Ghaffarzadeh Kermani ,  Radoje Drmanac

    IPC: G01N33/48 ,  G01N33/50 ,  G06F19/24 ,  G06F19/22

    Abstract: Methods, systems, and apparatuses are provided for creating and using a machine-leaning model to call a base at a position of a nucleic acid based on intensity values measured during a production sequencing run. The model can be trained using training data from training sequencing runs performed earlier. The model is trained using intensity values and assumed sequences that are determined as the correct output. The training data can be filtered to improve accuracy. The training data can be selected in a specific manner to be representative of the type of organism to be sequenced. The model can be trained to use intensity signals from multiple cycles and from neighboring nucleic acids to improve accuracy in the base calls.

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