Národní úložiště šedé literatury Nalezeno 4 záznamů.  Hledání trvalo 0.01 vteřin. 
My_Umi_Tool: Processing Of Unique Molecular Identifiers Without Mapping To A Reference Genome
Barilíková, Lujza
The presented paper describes a novel algorithm for processing unique molecular identifiers (UMIs) without mapping to a reference genome. For the past few years, there has been a rapid rise in the use of sequencing technologies and progress in bioinformatics tools. However, available tools for processing UMIs are usually relative computationally demanding and time-consuming which led us to design and develop a new algorithm as well as to implement some available software to provide an effective estimation of the total number of unique molecules. My_UMI_tool performs four major steps: preprocessing of an input file, clustering by UMIs, clustering by sequence similarity, and marking duplicates to generate final file.
Processing of Unique Molecular Identifiers without Mapping to a Reference Genome
Barilíková, Lujza ; Demko, Martin (oponent) ; Sedlář, Karel (vedoucí práce)
The main purpose of this thesis is to design a new algorithm for processing unique molecular identifiers (UMIs) without mapping to a reference genome. These random oligonucleotide sequences are attracting an increasing interest due to its ability to facilitate PCR error and bias recognition. Since there has been a rapid rise in the use of next-generation sequencing (NGS) technologies, great effort has been put into the development of tools for data analysis. At present, tools to solve these errors are usually relative time-consuming and complex due to computationally demanding alignment. The most important limitation of these tools lies in the fact that multi-mapping reads are allowed when processing duplicates. These reads are usually ignored and may lead to a reduction of quantitative accuracy and cause misleading interpretation of sequencing results. In order to solve this problem, a new approach is introduced in this thesis, which allows estimating the absolute number of unique molecules with relatively fast and reliable performance.
Methods Of Processing Oxford Nanopore Sequencing Data For Metagenomics
Barilíková, Lujza
The presented paper describes a new method of processing data produced by revolutionary sequencing technology introduced by Oxford Nanopore Technologies – MinION, which holds a great promise in the field of metagenomics. Low cost, produced long reads and portability, due to its small dimensions, represents only one of the many advantages of this technology. Despite of the benefits, there is a lack of available computational tools for handling the produced data and that is the reason, why a new method of processing such data should be created. In this study such method is created based on dimensionality reduction for data visualization.
Metody zpracování sekvenačních dat technologie Oxford Nanopore pro účely metagenomiky
Barilíková, Lujza ; Provazník, Ivo (oponent) ; Kupková, Kristýna (vedoucí práce)
Revolučná technológia sekvenovania od spoločnosti Oxford Nanopore Technologies – MinION, predstavuje veľkú nádej v oblasti metagenomiky. Nízka cena, produkovanie dlhých čítaní a prenosnosť, vďaka malým rozmerom, predstavuje len jednu z mnohých výhod tejto technológie. Napriek týmto benefitom je tu však nedostatok dostupných výpočtových nástrojov, ktoré by nám umožnili plne zaobchádzať s produkovanými dátami. V úvode tejto bakalárskej práce sú predstavené terajšie sekvenačné technológie so zameraním sa na technológie tretej generácie, predovšetkým na spomínané nanopórové sekvenovanie. V práci sú uvedené aj súčasné možnosti vizualizácie metagenomických dát. Hlavným cieľom tejto práce je vytvoriť algoritmus, ktorý za pomoci aplikácie metód redukcie dimenzionality priamo na surové dáta, produkované nanopórovým sekvenovaním, bude realizovať tzv. binning metagenomických vzoriek.

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