Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.

Abstract: The present disclosure provides methods of determining one or more tissues and/or cell-types contributing to cell-free DNA (“cfDNA”) in a biological sample of a subject. In some embodiments, the present disclosure provides a method of identifying a disease or disorder in a subject as a function of one or more determined more tissues and/or cell-types contributing to cfDNA in a biological sample from the subject.

Abstract: The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

Abstract: The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

Abstract: Current methods for annotating and interpreting human genetic variation typically exploit only a single information type (e.g., conservation) and/or are restricted in scope (e.g., to missense changes). Here, a method for objectively integrating many diverse annotations into a single measure (integrated deleteriousness score, or C-score) for each variant is described. The method may be implemented as a support vector machine (SVM) trained to differentiate high-frequency human-derived alleles from simulated variants. C-scores were precomputed for all 8.6 billion possible human single-nucleotide variants and allow scoring of short insertions-deletions. C-scores correlate with allelic diversity, annotations of functionality, pathogenicity, disease severity, experimentally measured regulatory effects and complex trait associations, and they highly rank known pathogenic variants within individual genomes.

Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.

Abstract: Computational methods used for large scale scaffolding of a genome assembly are provided. Such methods may include a step of applying a location clustering model to a test set of contigs to form two or more location cluster groups, each location cluster group comprising one or more location-clustered contigs; a step of applying an ordering model to each of the two or more location cluster groups to form an ordered set of one or more location-clustered contigs within each cluster group; and a step of applying an orienting model to each ordered set of one or more location-clustered contigs to assign a relative orientation to each of the location-clustered contigs within each location cluster group. In some aspects, the test set of contigs are generated from aligning a set of reads generated by a chromosome conformation analysis technique (e.g., Hi-C) with a draft assembly, a reference assembly, or both.

Abstract: Disclosed is a method for introducing a plurality of programmed nucleotide modifications into a single locus of a desired genomic DNA sequence in a single experiment. The method entails synthesizing a homology-directed repair (HDR) library comprising a plurality of oligonucleotides, wherein each oligonucleotide comprises a programmed nucleotide modification in the locus of the desired genome, and co-transfecting a population of cells with (i) an expression system capable of expressing Cas9 and a single guide RNA (sgRNA) and (ii) introducing a plurality of programmed nucleotide modifications to the locus of the desired genomic DNA sequence in one or more cells of the population. Also disclosed are methods for analyzing the functional consequence of a genomic mutation and for genomic screening.

Abstract: Methods and apparatus are provided for designing molecular inversion probes (MIPs). A computing device can determine representations of sequence features of a reference genome. The computing device can assess target arms that meet design criteria for a MIP in matching the representations of sequence features. For each pair of target arms that meet the design criteria, the computing device can: determine MIP performance data features for the pair, and determine a score for the pair using a MIP performance model operating on the MIP performance data features for the pair. The computing device can determine a subset of the target arms that collectively tile all of the sequence features, where the subset is determined based on the target arm scores. The computing device can determine designed MIPs based on the subset of target arms. The computing device can output information about each designed MIP.

Abstract: Disclosed is a method for multiplexed mutagenesis of a target nucleotide sequence. The method entails generating, in parallel, a set of mutagenic oligonucleotide primers designed to cover all or part of the target nucleotide sequence, and reacting the set of mutagenic oligonucleotide primers with the target sequence in the presence of a polymerase to generate a mutant nucleotide sequence library, wherein each member of the mutant nucleotide sequence library comprises a full-length copy of the target nucleotide sequence having a unique programmed mutation derived from one member of the set of mutagenic oligonucleotide primers. Also disclosed are methods for generating a mutant nucleotide sequence library and for generating a mutant protein library.

Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.

Abstract: The invention provides compositions and methods for preparing DNA sequencing libraries. In particular, the method relates to preparing DNA sequencing libraries from kilobase scale nucleic acids. The invention also provides methods for assembling short read sequencing data into longer contiguous sequences. The method is useful for various applications in genomics, including genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.

Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.

Abstract: The invention provides methods for preparing DNA sequencing libraries for assembling short read sequencing data into longer contiguous sequences and providing for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes. The methods generally comprise incorporating adaptor or vector sequences into at least one member of a target fragment library, amplifying the population of target fragment library members to produce a plurality of copies of amplified DNA molecules, fragmenting the plurality of amplified DNA molecules, incorporating additional adaptor sequences, and amplifying a region of at least one of the plurality of amplified DNA molecules. At least one resulting amplicon comprises a sequence identical to or complementary to at least a portion of a sequence tag and a sequence identical to or complementary to a portion of a target fragment library member.

Abstract: In some embodiments, methods of recovering a sequence-verified target nucleic acid are provided. In some embodiments, such methods may include tagging each member of a nucleic acid library with a set of adaptor sequences; sequencing the tagged members of the nucleic acid library; and recovering the sequence-verified target nucleic acid from the tagged and sequenced members of the nucleic acid library using a dial-out selection method. In certain embodiments, the members of the nucleic acid library may be tagged with a second set of adaptor sequences.

Abstract: This invention pertains to methods of imparting information onto nucleic acid sequences. In specific embodiments, the present invention provides site-specific recombinase systems and error-prone polymerase systems to alter nucleotide sequences such as DNA and mini-genomes, as well as for the production of microarrays. The present invention also provides methods of analyzing the modified nucleotides sequences provided herein. Methods of engineering and screening for novel modified polymerases that incorporate chain terminating nucleotides and/or labeled nucleotides more efficiently than wild-type polymerases are also provided.

Abstract: The invention provides compositions and methods for preparing DNA sequencing libraries. In particular, the method relates to preparing DNA sequencing libraries from kilobase scale nucleic acids. The invention also provides methods for assembling short read sequencing data into longer contiguous sequences. The method is useful for various applications in genomics, including genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.

Abstract: The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

Abstract: Methods and compositions for performing multiplex reactions are provided.

Abstract: Miniaturized, high-density, bead-based arrays are provided. Methods of producing and using clonal beads and producing and using miniaturized, high density, bead-based arrays are also provided.