Project detail

Real-time recognition of infection threats during nanopore sequencing

Duration: 01.02.2021 — 30.04.2022

Funding resources

Evropská unie - Interní grantová soutěž

- whole funder (2021-02-01 - 2022-04-30)

On the project

The project focused on the analysis of core genome variability in a closely related microbial population using nanopore sequencing technology and convolutional neural network. The uniqueness of the proposal is based on real-time identification, processing and analysis of genetic variability directly from raw sequencing signals without the need of lossy decoding. Thanks to that the sequencing can be stopped as sufficient data are gathered, and the crucial epidemiologic information is available immediately.

Mark

FEKT-K-21-6912

Default language

Czech

People responsible

Bartoň Vojtěch, Ing. - fellow researcher
Nykrýnová Markéta, Ing., Ph.D. - principal person responsible

Units

Department of Biomedical Engineering
- (2021-02-01 - 2022-04-30)
Faculty of Electrical Engineering and Communication
- (2021-02-01 - 2022-04-30)

Results

BARTOŇ, V.; NYKRÝNOVÁ, M.; ŠKUTKOVÁ, H. MANASIG: Python Package to MAnipulateNAnopore SIGnals from sequencing files. In 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2021. p. 1941-1947. ISBN: 978-1-6654-0126-5.
Detail

NOVÁK, V. Proceedings I of the 28th Conference STUDENT EEICT 2022 General papers. Proceedings I of the 28th Conference STUDENT EEICT 2022 General papers. 1. Brno: Brno University of Technology, Faculty of Electrical Engineering and Communication, 2022. ISBN: 978-80-214-6029-4.
Detail

NYKRÝNOVÁ, M.; JAKUBÍČEK, R.; BARTOŇ, V.; BEZDÍČEK, M.; LENGEROVÁ, M.; ŠKUTKOVÁ, H. Using deep learning for gene detection and classification in raw nanopore signals. Frontiers in Microbiology, 2022, vol. 13, no. 1, p. 1-11. ISSN: 1664-302X.
Detail

NYKRÝNOVÁ, M.; BARTOŇ, V.; VÍTEK, M.; BEZDÍČEK, M.; LENGEROVÁ, M.; ŠKUTKOVÁ, H. Raw nanopore squiggle alignment for bacterial typing distinction enhancement. In 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2021. p. 1969-1974. ISBN: 978-1-6654-0126-5.
Detail

Responsibility: Nykrýnová Markéta, Ing., Ph.D.