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Bioinformatics study of the third generation sequencing platforms applied on a thermophile
Umair, Mohammad ; Řeháková, Veronika ; Buchtikova, Iva ; Bezdicek, Matej ; Obruca, Stanislav ; Sedlář, Karel
This study compares the efficiency of Pacific Biosciences technology (PacBio) and Oxford Nanopore Technology (ONT) in sequencing, assembling, and annotating the Aneurinibacillus sp AFn2 bacterium. We aim to evaluate the performance based on contiguity, depth, and functional annotation of the resulting genome. Using ONT we generated 152,047 long reads assembling into 2 contigs with total base count of 0.4 billion which provided us efficient assembly while PacBio produced 139,701 reads, assembling into 21 contigs with a total base count of 1.4 billion. Functional annotation revealed differences in the number of coding sequences, with PacBio detecting more comprehensive gene sets than ONT. The comparative analysis done in this research shows the strengths and limitations of both the platforms, with ONT providing higher assembly contiguity and PacBio offering greater detail in genetic content. We aim to offer insights of both the sequencing technologies, guiding researchers in selecting the appropriate technology.
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Direct assembly of genome signals from nanopore sequencing
Karmazinová, Inna ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
The aim of this bachelor thesis is to search for overlaps between signals from nanopore sequencing using MinION device version R9. The theoretical part deals with methods used for genome assembly - greedy algorithm, overlap-layout-consensus (OLC) and de Bruijn graphs. Oxford Nanopore Technologies introduced the MinION device, which simplifies sequencing using the current change, which occurs while the DNA is passing through the nanopore. The error rate of the device is still high, the accuracy problem occurs during the base-calling. Using the difference signal, possibly also the dynamic time warping, it is possible to find overlaps between the individual signals. Signal analysis and genome assembly using the MinION signal could provide better accuracy.
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Direct assembly of genome signals from nanopore sequencing
Karmazinová, Inna ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
The aim of this bachelor thesis is to search for overlaps between signals from nanopore sequencing using MinION device version R9. The theoretical part deals with methods used for genome assembly - greedy algorithm, overlap-layout-consensus (OLC) and de Bruijn graphs. Oxford Nanopore Technologies introduced the MinION device, which simplifies sequencing using the current change, which occurs while the DNA is passing through the nanopore. The error rate of the device is still high, the accuracy problem occurs during the base-calling. Using the difference signal, possibly also the dynamic time warping, it is possible to find overlaps between the individual signals. Signal analysis and genome assembly using the MinION signal could provide better accuracy.
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