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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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Monotone functions avoiding majorities
Petr, Jan ; Barto, Libor (advisor) ; Mottet, Antoine (referee)
In the past five years, the Promise Constraint Satisfaction Problem (PCSP) has been a popular topic in computational complexity, covering a wide range of computational problems. In this work, we begin by introducing the PCSP and then turn our atten- tion to the still open problem of the PCSP over 'monotone folded Boolean structures'. Brakensiek and Guruswami showed in 2016 that the PCSP is in P if all odd majorities are polymorphisms between structures under consideration. We focus on the situation in which some of the odd majorities are not among the polymorphisms. We present a technique for proving NP-completeness of PCSPs that uses the notion of heavy sets. Our approach succeeds in proving that the absence of the 3-majority makes the PCSP NP-complete. We then give a few partial results for the case of the absence of the 5-majority. We finish by determining the size of the smallest heavy set for a particular family of functions. 1
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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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