Broadcom Corporation

Illumina Corporation

Broadcom Homenetworking, Inc.

Avago Technologies General IP (singapore) Pte. Ltd.

Edico Genome Corporation

Other

C-cube Microsystems, Inc.

Broadcom Corpotation

Illumina Software, Inc.

Avago Technologies General IP Pte, Ltd.

Eric Jon Ojard

Jason A Trachewsky

Edward H Frank

Rami Mehio

Gavin Derek Parnaby

John S Vieceli

Nitin Udpa

Jeyhan Karaoguz

Kevin H Peterson

Abde Ali Hunaid Kagalwalla

Joonsuk Kim

Sirikiat Lek Ariyavisitakul

Alan G Corry

John T Holloway

Thomas J Kolze

Bruce Joseph Currivan

Jonathan S Min

Daniel Harvey Howard

James Chi Thi

Pieter Van Rooyen

Michael D Ruehle

Mark Hahm

Gavin Stone

Amnon Ptashek

Matthew James Fischer

Henry S Ptasinski

Amit Goutam Bagchi

Bo Lu

Srinivasa H Garlapati

Ron Porat

Vinko Erceg

Peiman Amini

Carlos Horacio Aldana

David Garrett

Jun Zheng

Nihar Jindal

Joseph Paul Lauer

Tracy D Mallory

Raymond Hayes

Dorna Kashefhaghighi

Larry C Yamano

Varun Jain

John T Halloway

Jay Pattin

Amit Goutam

Alfonso Cano Pleite

Jacobus De Beer

Severine Catreux

Arun Visvanath

Sirikiat Ariyavistakul

The technology disclosed relates to state-based base calling. In particular, the technology disclosed relates to incorporating state information about data from previous sequencing cycles into the analysis of data from a current sequencing cycle when generating a base call for the current sequencing cycle. For example, when generating a base call for an Nth sequencing cycle, the technology disclosed can incorporate into the base calling logic state information about data from sequencing cycles 1 to N−1.

State-based base calling

A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing

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.

Intensity extraction for feature values in base calling

The technology disclosed relates to equalizer-based intensity correction for base calling. In particular, the technology disclosed relates to accessing an image whose pixels depict intensity emissions from a target cluster and intensity emissions from additional adjacent clusters, selecting a lookup table that contains pixel coefficients that are configured to increase a signal-to-noise ratio, applying the pixel coefficients to intensity values of the pixels in the image to produce an output, and base calling the target cluster based on the output.

Equalizer-based intensity correction for base calling

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.

Inter-cluster intensity variation correction and base calling

Intensity extraction from oligonucleotide clusters for base calling

The technology disclosed attenuates spatial crosstalk from sequencing images for base calling. The technology disclosed accesses a section of an image output by a biosensor, where the section of the image includes a plurality of pixels depicting intensity emission values from a plurality of clusters within the biosensor and from locations within the biosensor that are adjacent to the plurality of clusters. The plurality of clusters includes a target cluster. The section of the image is convolved with a convolution kernel, to generate a feature map comprising a plurality of features having a corresponding plurality of feature values. A weighted feature value is assigned to the target cluster, where the weighted feature value is based on one or more features values of the plurality of feature values of the feature map. The weighted feature value assigned to the target cluster is processed, to base call the target cluster.

Intensity extraction and crosstalk attenuation using interpolation and adaptation for base calling

The technology disclosed generates variation correction coefficients on a cluster-by-cluster basis to correct inter-cluster intensity profile variation for improved base calling. An amplification coefficient corrects scale variation. Channel-specific offset coefficients correct shift variation along respective intensity channels. The variation correction coefficients for a target cluster are generated based on combining analysis of historic intensity data generated for the target cluster at preceding sequencing cycles of a sequencing run with analysis of current intensity data generated for the target cluster at a current sequencing cycle of the sequencing run. The variation correction coefficients are then used to correct next intensity data generated for the target cluster at a next sequencing cycle of the sequencing run. The corrected next intensity data is then used to base call the target cluster at the next sequencing cycle.

Systems and methods for per-cluster intensity correction and base calling

The technology disclosed attenuates spatial crosstalk from sequencing images for base calling. In particular, the technology disclosed accesses an image whose pixels depict intensity emissions from a target cluster and intensity emissions from additional adjacent clusters. The pixels include a center pixel that contains a center of the target cluster. Each pixel in the pixels is divisible into a plurality of subpixels. Depending upon a particular subpixel, in a plurality of subpixels of the center pixel, which contains the center of the target cluster, the technology disclosed selects, from a bank of subpixel lookup tables, a subpixel lookup table that corresponds to the particular subpixel. The selected subpixel lookup table contains pixel coefficients that are configured to maximizes a signal-to-noise ratio. The technology disclosed element-wise multiplies the pixel coefficients with the pixels and determines a weighted sum.

Equalization-based image processing and spatial crosstalk attenuator

Bioinformatics systems, apparatuses, and methods for generating a De Brujin graph

Bioinformatics systems, apparatuses, and methods for generating a De Bruijn graph

Growing community of inventors

San Francisco, CA, United States of America

Eric Jon Ojard