Abstract: This disclosure relates to compositions and methods for generating a spatial array.

Abstract: This disclosure relates to methods for generating spatially barcoded arrays using concentration gradients.

Abstract: Methods for determining a location of a feature in a spatial array of features include: providing a spatial array including a plurality of features on a substrate, where a feature of the plurality of features has a capture probe, and where the capture probe has a spatial barcode and a constant sequence; hybridizing a first sequencing probe to the spatial barcode, where the first sequencing probe has a first label and a first nucleotide sequence; obtaining a first image of the first label with the first sequencing probe hybridized to the spatial barcode; determining, based on the first image, a first portion of a sequence of the spatial barcode; and associating the feature with a location in the spatial array based on a location of the first label in the first image.

Abstract: Determination of a nucleic acid sequence using sequence reads of the nucleic acid. The reads, in sets of reads, include a first portion for a subset of the nucleic acid and a common second portion identifying a reaction partition that formed the read, where the partition has the subset of the nucleic acid in the form of a fragment. A set of k-mers is created for a read, with identifiers of the source reads for each k-mer are retained. The k-mers are used to determine whether to derive a contig sequence representative of the nucleic acid, where the contig comprises an origin node comprising a first set of overlapping k-mers and one of a first destination node comprising a second set of overlapping k-mers and a second destination node comprising a third set of overlapping k-mers. The sequence of the nucleic acid is assembled using at least the contig.

Abstract: Systems and methods for determining structural variation and phasing using variant call data obtained from nucleic acid of a biological sample are provided. Sequence reads are obtained, each comprising a portion corresponding to a subset of the test nucleic acid and a portion encoding a barcode independent of the sequencing data. Bin information is obtained. Each bin represents a different portion of the sample nucleic acid. Each bin corresponds to a set of sequence reads in a plurality of sets of sequence reads formed from the sequence reads such that each sequence read in a respective set of sequence reads corresponds to a subset of the nucleic acid represented by the bin corresponding to the respective set. Binomial tests identify bin pairs having more sequence reads with the same barcode in common than expected by chance. Probabilistic models determine structural variation likelihood from the sequence reads of these bin pairs.

Abstract: Provided herein are compositions, systems and methods for tagging molecular events, reactions, species, etc., but without the need for complex, highly diverse libraries of tagging molecules. Provided are tagging moieties that can have a smaller number, a few, or even a single original “tagging” structure that may be transformed or transformable, in situ, into a collection of larger numbers of unique tagging or “barcode” moieties.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from a single cell. Such polynucleotide processing may be useful for a variety of applications. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins) and chromatin (e.g., accessible chromatin).

Abstract: The present invention is directed to methods, compositions and systems for capturing and analyzing sequence information contained in targeted regions of a genome. Such targeted regions may include exomes, partial exomes, introns, combinations of exonic and intronic regions, genes, panels of genes, and any other subsets of a whole genome that may be of interest.

Abstract: The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.

Abstract: The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.

Abstract: Described are computer-implemented methods, systems, and media for de novo phased diploid assembly of nucleic acid sequence data generated from a nucleic acid sample of an individual utilizing nucleic acid tags to preserve long-range sequence context for the individual such that a subset of short-read sequence data derived from a common starting sequence shares a common tag. The phased diploid assembly is achieved without alignment to a reference sequence derived from organisms other than the individual. The methods, systems, and media described are computer-resource efficient, allowing scale-up.

Abstract: This disclosure provides microwell capsule array devices. The microwell capsule array devices are generally capable of performing one or more sample preparation operations. Such sample preparation operations may be used as a prelude to one more or more analysis operations. For example, a device of this disclosure can achieve physical partitioning and discrete mixing of samples with unique molecular identifiers within a single unit in preparation for various analysis operations. The device may be useful in a variety of applications and most notably nucleic-acid-based sequencing, detection and quantification of gene expression and single-cell analysis.

Abstract: Methods and systems are provided for sample preparation techniques and sequencing of macromolecular constituents of cells and other biological materials.

Abstract: Compositions, processes and systems are provided for preparing and analyzing sample indexing of nucleic acid libraries for multiplexed sequencing analysis of diverse sample sets.

Abstract: The present disclosure provides methods and systems for generation of compositions comprising two or more sets of molecules. Compositions herein may comprise sets of molecules of different types. Sets of molecules may be generated by attachment to supports. Different types of molecules may be used to generate a large number of unique molecules. One or more types of molecules may be used to identify one or more additional types of molecules. Compositions of the present disclosure may be used in, for example, nucleic acid sequencing.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Abstract: The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from a single cell. Such polynucleotide processing may be useful for a variety of applications. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins) and chromatin (e.g., accessible chromatin).

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.