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Mapping techniques for reference-based genome assembly
Petrovský, Jan ; Sedlář, Karel (referee) ; Bartoň, Vojtěch (advisor)
The bachelor thesis deals with the tools used to map the genome to the reference sequence. The theoretical part describes the currently used sequencing technologies, whether the first generation or the latest technologies of the third generation, an overview of the tools used for de novo genome construction, approaches and tools used for mapping to the reference, the ART program and related data formats. The practical part consists of creating a test dataset of NGS data and creating appropriate metrics to evaluate the quality of the mapping and their subsequent usage on the chosen mapping tools.
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3D analysis of biological samples using focused ion beam electron microscopy
Petrovský, Jan ; Sobola, Dinara (referee) ; Hrubanová,, Kamila (advisor)
Understanding the three-dimensional information inside biological microscopic structures is easier and more intuitive than a set of two-dimensional images. The aim of this thesis is to create a 3D model of the bacterium Rubrum rhodospirillum that allows the observation of structural changes with respect to the whole experiment. To successfully image the cells, it is essential to fix their ultrastructures. In our case, chemical fixation followed by heavy metal staining and embedding in resin is used. The final acquisition of a good quality dataset for the creation of the three-dimensional model is preceded by the optimization of the image acquisition parameters. Emphasis is placed on the parameters of the electron and ion beam used. In this work, several different microscope settings are tested and compared and their influence on the final image is examined. Subsequently, several datasets are imaged using the software Auto Slice and View 4 and then whole cells and PHB granules inside these cells are segmented. From this modified data, a 3D model of the bacteria in the studied volume was created using selected reconstruction techniques.
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Mapping techniques for reference-based genome assembly
Petrovský, Jan ; Sedlář, Karel (referee) ; Bartoň, Vojtěch (advisor)
The bachelor thesis deals with the tools used to map the genome to the reference sequence. The theoretical part describes the currently used sequencing technologies, whether the first generation or the latest technologies of the third generation, an overview of the tools used for de novo genome construction, approaches and tools used for mapping to the reference, the ART program and related data formats. The practical part consists of creating a test dataset of NGS data and creating appropriate metrics to evaluate the quality of the mapping and their subsequent usage on the chosen mapping tools.
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