Illumina Corporation

Illumina Cambridge Limited

Anthony James Cox

John A Moon

Francisco Jose Garcia

Stephen Tanner

Tobias Mann

Klaus Maisinger

Michael Lawrence Parkinson

Haifang H Ge

Kai-How Farh

Ole Schulz-Trieglaff

Dirk Evers

Lilian Janin

Markus J Bauer

Giovanna Rosone

Ole Benjamin Schulz-Trieglaff

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.

Creating a template of nucleic acid site locations on a flow cell

Analyzing image data from nucleic acid sequencing

Identifying nucleotides by determining phasing

The technology disclosed directly operates on sequencing data and derives its own feature filters. It processes a plurality of aligned reads that span a target base position. It combines elegant encoding of the reads with a lightweight analysis to produce good recall and precision using lightweight hardware. For instance, one million training examples of target base variant sites with 50 to 100 reads each can be trained on a single GPU card in less than 10 hours with good recall and precision. A single GPU card is desirable because it a computer with a single GPU is inexpensive, almost universally within reach for users looking at genetic data. It is readily available on could-based platforms.

Deep learning-based variant classifier

System and methods for identifying nucleotides

Data processing system and methods

The present disclosure provides computer implemented methods and systems for analyzing datasets, such as large data sets output from nucleic acid sequencing technologies. In particular, the present disclosure provides for data analysis comprising computing the BWT of a collection of strings in an incremental, character by character, manner. The present disclosure also provides compression boosting strategies resulting in a BWT of a reordered collection of data that is more compressible by second stage compression methods compared to non-reordered computational analysis.

Methods and systems for data analysis and compression

Methods and systems for data analysis using the Burrows Wheeler transform

Growing community of inventors

Essex, United Kingdom

Anthony James Cox