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Advanced Computational Methods for Increasing the Discriminatory Power of Genotyping Methods
Nykrýnová, Markéta ; Budinská, Eva (oponent) ; Hrabák,, Jaroslav (oponent) ; Škutková, Helena (vedoucí práce)
This dissertation aims at developing new computational methods to increase the discriminatory power of genotyping methods. The main focus is on distinguishing closely related bacterial strains, e.g. from the same hospital or ward. The first part of the thesis describes current typing methods and new approaches to identify genetic markers with high levels of sequence variability that contribute to distinguishing bacterial populations better. The proposed methods are based on the entropy signal calculation and analysis of unmapped reads. The second part of the thesis deals with designing new methods for raw nanopore sequencing data processing; thus, it can be used for rapid high-sensitivity bacterial typing without the need to convert current signals into nucleotide sequences. Overall, this dissertation contributes to the improvement and refinement of routine typing methods by utilizing the proposed bioinformatics approaches and presenting a unique application for experimental nanopore sequencing in rapid genotyping and bacteria analysis.

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