Method for improving the consensus sequence from NGS data based on reads classification

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F19%3APU133506" target="_blank" >RIV/00216305:26220/19:PU133506 - isvavai.cz</a>

Result on the web

<a href="http://www.radio.feec.vutbr.cz/ieee/userfiles/downloads/archive/2019-Mikulov/sbornik.pdf" target="_blank" >http://www.radio.feec.vutbr.cz/ieee/userfiles/downloads/archive/2019-Mikulov/sbornik.pdf</a>

DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Method for improving the consensus sequence from NGS data based on reads classification

Original language description

Nowadays, next-generation sequencing is on the rise as a cost of sequencing is constantly dropping. However, the processing of the sequence data remains problematic as the algorithms for reference-based assembly are both computationally and time-demanding. Moreover, resulting assembly is still imperfect. In this paper, we present a new method for improving the quality of the consensus sequence from the assembled data. We examine the regions in the consensus sequence, which show a high number of ambiguous nucleotides. Using a classification of reads covering these regions, we try to reduce the number of ambiguous nucleotides in the consensus. This improved consensus sequence then can be used for bacteria typing and precise discrimination of bacteria strains.

Czech name

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Czech description

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Type

D - Article in proceedings

CEP classification

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OECD FORD branch

30403 - Technologies involving identifying the functioning of DNA, proteins and enzymes and how they influence the onset of disease and maintenance of well-being (gene-based diagnostics and therapeutic interventions [pharmacogenomics, gene-based therapeutics])

Project

<a href="/en/project/GA17-01821S" target="_blank" >GA17-01821S: High throughput bacterial genome assembly and annotation techniques using genomic signal processing</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2019

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Article name in the collection

Proceedings of IEEE Student Branch Conference Mikulov 2019

ISBN

978-80-214-5781-2

ISSN

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e-ISSN

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Number of pages

4

Pages from-to

6-9

Publisher name

Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních technologií

Place of publication

Brno

Event location

Mikulov, Czech republic

Event date

Sep 9, 2019

Type of event by nationality

EUR - Evropská akce

UT code for WoS article

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