Patents Assigned to ILLUMINA SOFTWARE, INC.
  • Publication number: 20230420074
    Abstract: Systems, methods, and apparatus are described herein for identifying callable regions and performing variant calling while operating within allocated memory. A sequencing subsystem may comprise a variant caller or variant caller subsystem. The variant caller may include a calling subsystem configured to identify callable regions and may send the callable regions to a downstream genotyping subsystem of the variant caller. The calling subsystem of the variant caller may be configured to detect a callable region of the sequencing data when a depth of the plurality of reads is above a callable region depth threshold. The calling subsystem of the variant caller may monitor memory used by the callable region and, when the memory used exceeds a memory threshold of a total amount of memory allocated, the calling subsystem may split or spill at least a portion of the callable region to operate within the total amount of allocated memory.
    Type: Application
    Filed: June 23, 2023
    Publication date: December 28, 2023
    Applicants: ILLUMINA SOFTWARE, INC., Illumina Cambridge Limited
    Inventors: Adam Michael Birnbaum, Fabian Jobst Klötzl, Arun Visvanath
  • Publication number: 20230041989
    Abstract: A method of base calling using at least two base callers is disclosed. The method includes executing at least a first base caller and a second base caller on sensor data generated for sensing cycles in a series of sensing cycles; generating, by the first base caller, first classification information associated with the sensor data, based on executing the first base caller on the sensor data; and generating, by the second base caller, second classification information associated with the sensor data, based on executing the second base caller on the sensor data. In an example, based on the first classification information and the second classification information, a final classification information is generated, where the final classification information includes one or more base calls for the sensor data.
    Type: Application
    Filed: July 28, 2022
    Publication date: February 9, 2023
    Applicant: ILLUMINA SOFTWARE, INC.
    Inventors: Gavin Derek PARNABY, Mark David HAHM
  • Publication number: 20230029970
    Abstract: A method of generating base calls by a base caller is disclosed. The method includes receiving a plurality of sensor data from a flow cell, wherein the plurality of sensor data is within a first range and identifying a second range, such that at least a threshold percentage of the plurality of sensor data are within the second range. At least a subset of the plurality of sensor data, that are within the second range, are mapped to a third range, thereby generating a plurality of normalized sensor data. The plurality of normalized sensor data is processed in a base caller, to call, for the plurality of normalized sensor data, one or more corresponding bases.
    Type: Application
    Filed: June 13, 2022
    Publication date: February 2, 2023
    Applicants: ILLUMINA, INC., ILLUMINA SOFTWARE, INC.
    Inventors: Rohan PAUL, Dorna KASHEFHAGHIGHI, John S. VIECELI, Andrew Dodge HEIBERG
  • Publication number: 20230015945
    Abstract: The technology disclosed extracts intensities from sequencing images for base calling target clusters and attenuates spatial crosstalk from neighboring clusters. The technology disclosed accesses a particular section from a plurality of sections of an image output by a sensor, the particular section of the image including at least one pixel depicting intensity emission values from a target cluster and neighboring clusters located across the sensor, and convolves the particular section of the image with a corresponding convolution kernel in a plurality of convolution kernels, to generate a feature map comprising a plurality of feature values. The technology disclosed further assigns a corresponding feature value to the target cluster based on feature values in the plurality of feature values adjoining a center of the target cluster, and processes the corresponding feature value assigned to the target cluster, to base call the target cluster.
    Type: Application
    Filed: September 2, 2022
    Publication date: January 19, 2023
    Applicant: ILLUMINA SOFTWARE, INC.
    Inventors: Abde Ali Hunaid KAGALWALL, Eric Jon OJARD, Rami MEHIO, Gavin Derek PARNABY, Nitin UDPA, Bo LU, John S. VIECELI
  • Publication number: 20230018469
    Abstract: We disclose a system. The system comprises a memory and a runtime logic. The memory stores a plurality of specialist signal profilers. Each specialist signal profiler in the plurality of specialist signal profilers is trained to maximize signal-to-noise ratio of sequenced signals in a particular signal profile detected for analytes in a particular analyte class and characterized in a particular training data set. The runtime logic, having access to the memory, is configured to execute a base calling operation by applying respective specialist signal profilers in the plurality of specialist signal profilers to sequenced signals in respective signal profiles detected for analytes in respective analyte classes during the base calling operation.
    Type: Application
    Filed: June 13, 2022
    Publication date: January 19, 2023
    Applicant: ILLUMINA SOFTWARE, INC.
    Inventors: Abde Ali Hunaid KAGALWALLA, Eric Jon OJARD, Rami MEHIO, Gavin Derek PARNABY, Nitin UDPA, John S. VIECELI
  • Publication number: 20220300811
    Abstract: A method of quantizing parameters of a neural network includes grouping a plurality of parameters of a neural network in a plurality of groups. Each group of the plurality of groups includes corresponding two or more parameters of the plurality of parameters. In an example, for each group, a corresponding quantization format is selected from a plurality of available quantization formats, such that a first quantization format selected for at least a first group is different from a second quantization format selected for at least a second group. For each group, individual parameters within the corresponding group are quantized using the quantization format selected for the corresponding group. The quantized parameters of the plurality of groups are stored in a memory.
    Type: Application
    Filed: March 4, 2022
    Publication date: September 22, 2022
    Applicant: ILLUMINA SOFTWARE, INC.
    Inventor: Gavin Derek PARNABY