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Martin Smith

‘Squiggle'-cell sequencing

About Martin Smith

Martin Smith is currently the head of the Genomic Technologies program at The Kinghorn Centre for Clinical Genomics, part of the Garvan Institute of Medical Research in Sydney, Australia. His group works closely with the newly established Garvan-Weizmann Centre for Cellular Genomics. Martin completed his PhD in genomics and computational biology in 2012 at the Institite for Molecular Bioscience, University of Queensland. He is originally from Montreal, where he studied Bioinformatics (MSc) and Microbiology (BSc). 

Abstract

ONT offers more than ultra long reads and the capacity to detect base modifications in real-time. I will elaborate on the real-time nature of nanopore sequencing, where biopolymer subsequences can be interrogated directly as they transit through the pore. To achieve this, it is essential to venture into ‘squiggle space’—the raw or normalised signal data produced by nanopore flowcells. I will describe a method to de-multiplex barcodes in squiggle space, using supervised and unsupervised approaches. So far, this approach performs well on standard ONT barcodes, and more than doubles the amount of correctly demultiplexed barcodes from single cell RNAseq data when compared to standard barcode matching strategies. Furthermore, I will demonstrate how this approach can be used to improve the assembly of full-length cDNAs from thousands of cells.

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