Seminar • Bioinformatics • Nanopore Sequencing: Why Do We Like Raw Signal?Export this event to calendar

Wednesday, May 18, 2022 — 10:30 AM to 11:30 AM EDT

Please note: This seminar will be presented in person in DC 1304 as well as streamed online.

Tomáš Vinař, Department of Applied Informatics
Comenius University in Bratislava, Slovakia

MinION sequencers from Oxford Nanopore are pocket size USB-connected devices that can be used in many applications from virus genomic surveillance to on-site sequencing at the International Space Station. As DNA passes through nanopores embedded in the device, it produces a raw electrical signal which is then translated to a sequence through computational process called base calling, typically employing deep neural networks. In many computational pipelines, base calling is a bottleneck, both from the point of view of accuracy and computational time.

I will first talk about methods that we have developed to make base calling more efficient. In the second part, we will introduce some problems where base calling can be skipped altogether by analyzing the raw sequencing signals directly.

Joint work with Broňa Brejová, Vlado Boza, Peter Perešíni, Jozef Sitarčík.


To join this seminar on Zoom, please go to https://uwaterloo.zoom.us/j/94482358564.

Location 
DC - William G. Davis Computer Research Centre
Hybrid: DC 1304 | Online seminar
200 University Avenue West

Waterloo, ON N2L 3G1
Canada
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