Abstract: Resolution of images used in processes such as sequencing by synthesis may be increased by structuring sites that would emit signals in the images to have different elevations. Differences in focus caused by these differences in elevation may be used to filter out background illumination, thereby providing an image in which in focus sites may be resolved even though the separation between any site and its nearest neighbor may be below the diffraction limit of the light that would be emitted.

Abstract: The disclosure provides a structured illumination imaging system that utilizes an image sensor (e.g., an active pixel sensor) in an active plane of a patterned sample to increase image resolution. The imaged sample may be patterned and/or aligned over an image sensor such that each light sensor (e.g., pixel) of the image sensor has a respective plurality of features formed and/or mounted above it. In response to illumination, each of the features may emit fluorescent light that is collected by a pixel of the image sensor. During imaging, each pixel of the image sensor may be spatially multiplexed using structured illumination such that only a subset (e.g., one or two) of the features aligned over the pixel are illuminated with structured light during an image read.

Abstract: Temperature-controllable reagent cartridges and systems for controlling the temperature in such reagent cartridges are provided. An example such system may include a reagent cartridge having reagent reservoirs located at least in part within an interior plenum volume of a cartridge housing. In such an example system, each reagent reservoir may be defined, in part, by a sidewall, and a first reagent reservoir may be spaced apart from a second reagent reservoir to form a fluid flow passage between corresponding sidewalls thereof. A fluid inlet through the cartridge housing may be provided that fluidically connects the interior plenum volume with a fluid supply port of a temperature control system of an analysis instrument when the reagent cartridge is received by the analysis instrument; a fluid outlet through the cartridge housing that fluidically connects the interior plenum volume with a fluid return port of the temperature control system may also be provided.

Abstract: The disclosure provides methods for creating long oligonucleotide reagents that include barcodes and other element for sequencing library preparation, where the oligonucleotides are created by multiple tiers of ligation of shorter oligos. The disclosed methods work to extend short oligos that are attached to particles, thereby allowing one to create particles that carry large number of long sample preparation oligonucleotides without being required to synthesize those full-length molecules with a polymerase.

Abstract: A flow cell assembly is provided that includes a support layer of low-background material, a film of anodized metal oxide (AMO) material adhered to the support layer, and a substrate formed, in part, by one or more patterns imparted in the AMO material. A flow cell assembly herein may include a support layer of low-background material, a film of AMO material adhered to the support layer, and a substrate surface comprising one or more patterns imparted in the AMO material. Each pattern may comprise an array of nanowell features surrounded by interstitial regions of featureless AMO film.

Abstract: We propose a neural network-implemented method for base calling analytes. The method includes accessing a sequence of per-cycle image patches for a series of sequencing cycles, where pixels in the image patches contain intensity data for associated analytes, and applying three-dimensional (3D) convolutions on the image patches on a sliding convolution window basis such that, in a convolution window, a 3D convolution filter convolves over a plurality of the image patches and produces at least one output feature. The method further includes beginning with output features produced by the 3D convolutions as starting input, applying further convolutions and producing final output features and processing the final output features through an output layer and producing base calls for one or more of the associated analytes to be base called at each of the sequencing cycles.

Abstract: The present disclosure relates to methods, compositions, and kits for treating target nucleic acids, including methods and compositions for fragmenting and tagging nucleic acid (e.g., DNA) using transposome complexes bound to a solid support.

Abstract: Cloud provider accounts can be integrated into a software-as-a-service platform. Configuration options can be provided to support various levels of granularity so that different cloud provider accounts can be provided to different tenants, workgroups, users, applications, and the like. From a user perspective, the fact that data is being stored at a cloud provider account can be transparent in that the same features and authentication process can be supported across different cloud provider types. In practice, limited temporary derived credentials can be generated from underlying credentials to provide fine-grained control of access to cloud provider account resources while avoiding administrative overhead.

Abstract: Presented herein are altered polymerase enzymes for improved incorporation of nucleotides and nucleotide analogues, in particular altered polymerases that maintain high fidelity under reduced incorporation times, as well as methods and kits using the same.

Abstract: Presented herein are methods and compositions for targeted amplification of DNA and sample identification. The methods are particularly useful in validation and quality control of samples and to confirm that WGS sequence data is properly paired with a patient sample prior to delivering sequence data to a physician or to a patient.

Abstract: Embodiments of the present disclosure relate to nucleotide molecules with a 3? AOM blocking group. Also provided herein are methods to prepare such nucleotide molecules, and the uses of fully functionalized nucleotides containing the 3?-OH blocking group for sequencing applications.

Abstract: Disclosed herein are systems and methods for collapsing sequencing reads and identifying similar sequencing reads. In one example, a method includes generating a plurality of first identifier subsequences from a first identifier sequence of each nucleotide sequencing read and generating a first signature for the nucleotide sequencing read by applying hashing to the plurality of first identifier subsequences. The method may include assigning the nucleotide sequencing read to a first particular bin of a first data structure based on the first signature and determining a nucleotide sequence for each first particular bin of the first data structure with one or more nucleotide sequencing reads assigned.

Abstract: Embodiments provided herein relate to methods and compositions for preparing nucleic acid libraries. Some embodiments include preparing libraries from nucleic acids obtained from degraded samples, such as ancient samples and fixed samples.

Abstract: An apparatus includes one or more valves adapted to be coupled to corresponding reagent reservoirs and a flow cell interface adapted to be coupled to a flow cell. The apparatus includes a sample cartridge interface having one or more ports and adapted to be coupled to a sample cartridge carrying a sample of interest. The sample cartridge interface positioned downstream of the flow cell interface. The apparatus includes a pump adapted to load a channel of the flow cell with the sample of interest via the flow cell interface associated with an outlet of the flow cell and a corresponding port of the sample cartridge interface.

Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

Abstract: Biosensor including an array of reaction sites and corresponding light sensors may experience crosstalk in which photons from one reaction site are detected by neighbors of its corresponding light sensor, and such crosstalk may be corrected using sharpening kernels corresponding to the sensors in the array. Such sharpening kernels may be derived from generative matrices, which themselves may be derived from point spread functions representing dispersion of illumination emitted from the reaction sites.

Abstract: The technology disclosed corrects inter-cluster intensity profile variation for improved base calling on a cluster-by-cluster basis. The technology disclosed accesses current intensity data and historic intensity data of a target cluster, where the current intensity data is for a current sequencing cycle and the historic intensity data is for one or more preceding sequencing cycles. A first accumulated intensity correction parameter is determined by accumulating distribution intensities measured for the target cluster at the current and preceding sequencing cycles. A second accumulated intensity correction parameter is determined by accumulating intensity errors measured for the target cluster at the current and preceding sequencing cycles. Based on the first and second accumulated intensity correction parameters, next intensity data for a next sequencing cycle is corrected to generate corrected next intensity data, which is used to base call the target cluster at the next sequencing cycle.