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Influence of second and third generation sequencers on cgMLST analysis of closely-related bacterial strains.
Slavíček, David ; Sedlář, Karel (referee) ; Nykrýnová, Markéta (advisor)
This bachelor thesis is about influence of sequncers of second and third generationon cgMLST analysis of bacterial genome. In the theoretical section were described selected sequencers of second and third generation and genome assembly principles. In the practical part were assembled six genomes of Klebsiella pneumoniae bacteria from University Hospital Brno. The genomes were sequenced each on two different sequencers, Illumina Miseq and Oxford Nanopore Technologies Minion. The genomes were assembled. Suitable genes were selected and insufficient quality genomes removed for the cgMLST analysis. The cgMLST analysis was performed and the results are shownin graphs.
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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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Analysis of the dicyemid diversity using amplicon sequencing
FLEGROVÁ, Tereza
Using amplicon sequencing, this study reveals dicyemid diversity around the world as well as within individual cephalopod hosts. A wide number of samples of multiple species were collected to reflect true dicyemid diversity. Heterogeneity primers were designed in order to improve the sequencing performance of the Illumina platform. A complex bioinformatic pipeline was implemented to process non-overlapping reads. The species delimitation methods were used to categorize occurring dicyemid types. Using the output of implemented methods, dicyemid diversity was assessed, proposing new trends opposing the current methodology.
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Application of next-generation sequencing for phylogenetic reconstruction of polyploid plants
Skopalíková, Jana ; Fér, Tomáš (advisor) ; Šrámková, Gabriela (referee)
This bachelor thesis summarizes available information about currently used next- generation sequencing (NGS) methods where a big progress was achieved during last few years. Great advantage of NGS is the ability to gain huge amount of data at much lower cost per base compared to the Sanger sequencing. However, there are various pitfalls in data analysis. Nowadays it is possible to sequence the entire genomes of individuals. Nevertheless, this approach remains challenging when studying many individuals, e.g. in phylogenetics. Recently, several approaches for effective reduction of genome complexity arose: transcriptome sequencing (RNA-Seq), target enrichment, restriction digest-based methods (RAD-Seq, RLL, GBS), genome skimming (shallow sequencing), etc. Each method has both advantages and disadvantages that affect its utility in phylogenetics. Furthermore, the thesis deals with polyploid speciation and particularity of phylogenetics in polyploid plants - selection of suitable markers followed by data processing and phylogenetic analyzes. The last part of the thesis is devoted to my future research of polyploid genus Curcuma L.
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Influence of second and third generation sequencers on cgMLST analysis of closely-related bacterial strains.
Slavíček, David ; Sedlář, Karel (referee) ; Nykrýnová, Markéta (advisor)
This bachelor thesis is about influence of sequncers of second and third generationon cgMLST analysis of bacterial genome. In the theoretical section were described selected sequencers of second and third generation and genome assembly principles. In the practical part were assembled six genomes of Klebsiella pneumoniae bacteria from University Hospital Brno. The genomes were sequenced each on two different sequencers, Illumina Miseq and Oxford Nanopore Technologies Minion. The genomes were assembled. Suitable genes were selected and insufficient quality genomes removed for the cgMLST analysis. The cgMLST analysis was performed and the results are shownin graphs.
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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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Use of microbial community structure as a marker of conditions in underground biotops
Burkartová, Kateřina ; Falteisek, Lukáš (advisor) ; Drahota, Petr (referee)
The amount of data obtained by barcoding of prokaryotic 16S rDNA from natural habitats is increasing exponentially. Thus, methods enabling us to extract useful information from these data are of increasing importance. In this thesis microbial communities from water, sludge and drilling dust were analyzed by 16S rDNA sequencing in three geologically well described sedimentary aquifers in Bohemian Massif. The main goal of this research was to establish how different analytical approaches can be useful in interpretation of groundwater biogeochemical processes. Three approaches were used: First, taxonomy and metabolic traits of the most abundant microorganisms were assessed. Second, ordination methods showing metabolic and taxonomic variability between communities were used. Last the analysis of phylogenetic dissimilarity using UniFrac metrics was performed. When analyzing individual localities separately, the shift in microbial community composition corresponds with the change of environmental conditions. The unconstrained ordination method based on the variability in metabolic traits indicated, that sludge samples are more informative than water samples when asking which electron donor is used in microbial communities. On the other hand, unconstrained ordination methods were useless when the...
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