10x Genomics, Inc.

Alexander Y Wong

David Luther Alan Stafford

Adam David Azarchs

Paul Ryvkin

Kevin J Wu

Michael Schnall-Levin

Patrick Marks

Preyas Shah

Niranjan Srinivas

David Stafford

A system for providing structural variation or phasing information is provided. The system accesses a nucleic acid sequence dataset corresponding to a target nucleic acid in a sample. The dataset comprises a header, synopsis, and data section. The data section comprises a plurality of sequencing reads. Each sequencing read comprises a first portion corresponding to a subset of the target nucleic acid and a second portion that encodes an identifier for the sequencing read from a plurality of identifiers. One or more programs in the memory of the system use a microprocessor of the system to provide a haplotype visualization tool that receives a request for structural variation or phasing information from the dataset. The request is evaluated against the synopsis thereby identifying portions of the data section. Structural variation or phasing information is formatted for display in the haplotype visualization tool using the identified portions of the data section.

Systems and methods for visualizing structural variation and phasing information

A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.

Systems and methods for visualizing a pattern in a dataset

Methods for screening clonotypes are provided. Data representing a plurality of cells from a single subject is obtained. The data represents a plurality of clonotypes. The data includes a plurality of contigs for each respective clonotype in the plurality of clonotypes. Each respective contig in the plurality of contigs comprises (i) an indication of chain type for the respective contig and (ii) a contig sequence of an mRNA of the respective cell. There is determined, using the data, for each respective clonotype in the plurality of clonotypes, a number of the plurality of cells that represent the respective clonotype. In some instances, more than one cell in the plurality of cells have the same clonotype in the plurality of clonotypes. In some instances, the plurality of clonotypes comprises 25 clonotypes and where the plurality of cells includes at least one cell for each clonotype in the plurality of clonotypes.

Systems and methods for clonotype screening

A computer implemented system for genomic data sorting, comprising alignment and position mapping. The system maps each read to a position on the reference genome with which the read is associated, followed by sorting these reads by their mapped positions.

Methods and apparatus for sorting data

Methods, computer readable media, and systems service a queue, comprising a plurality of jobs, by identifying nodes satisfying a hardware requirement for at least a subset of jobs in the queue. Each job indicates when it was submitted to the queue and one or more node resource requirements. A current availability score for each node class in a plurality of node classes is determined and nodes of a first node class in the plurality of node classes are reserved when a demand score for the class satisfies the current availability score for the first node class by a first threshold amount. Reserved nodes are permitted to draw jobs from the queue in accordance with satisfaction by such nodes of the node resource requirements of the jobs but are terminated, without completing the jobs, when the current availability score for their node class exceeds a second threshold amount.

Systems and methods for distributed resource management

Methods, nontransitory computer readable media, and systems are disclosed for servicing a job queue. Each job has node resource requirements. Composite job memory and processor requirements is determined from these requirements. Nodes that satisfy these requirements are identified by obtaining, for each class of a plurality of node classes: an availability score, a number of processers, and a memory capability. A request for nodes of a class is made when a demand score for the class satisfies the class availability score. An acknowledgement and updated availability score is received upon request acceptance. A declination is received upon request rejection. The submitting and receiving is performing multiple times, if needed, until each class has been considered for a request or sufficient acknowledgements are received to satisfy the composite requirements of the jobs. Each node in the cluster draws jobs from the queue subject to the collective requirements of the drawn jobs.

Methods, nontransitory computer readable media, and systems are disclosed for servicing a job queue. Each job has node resource requirements. Composite job memory and processor requirements is determined from these requirements. Nodes that satisfy these requirements are identified by obtaining, for each class of a plurality of node classes: an availability score, a number of processors, and a memory capability. A request for nodes of a class is made when a demand score for the class satisfies the class availability score. An acknowledgement and updated availability score is received upon request acceptance. A declination is received upon request rejection. The submitting and receiving is performing multiple times, if needed, until each class has been considered for a request or sufficient acknowledgements are received to satisfy the composite requirements of the jobs. Each node in the cluster draws jobs from the queue subject to the collective requirements of the drawn jobs.

A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity in a plurality of first entities for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters. Differences in the discrete attribute values for the first entity across the second entities of a given cluster relative to the discrete attribute value for the same first entity across the other clusters are computed thereby deriving differential values. A heat map of these differential values for each first entity for each cluster is displayed to reveal the pattern in the dataset.

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San Francisco, CA, United States of America

Alexander Y Wong