Publication result detail

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

NYKRÝNOVÁ, M.; ŠKUTKOVÁ, H.

Original Title

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

English Title

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

Type

Paper in proceedings (conference paper)

Original Abstract

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.

English abstract

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.

Keywords

sequencing; ambiguous nucleotides; genome assembly; consensus calling; cluster analysis

Key words in English

sequencing; ambiguous nucleotides; genome assembly; consensus calling; cluster analysis

Authors

NYKRÝNOVÁ, M.; ŠKUTKOVÁ, H.

RIV year

2020

Released

09.09.2019

Publisher

Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních technologií

Location

Brno

ISBN

978-80-214-5781-2

Book

Proceedings of IEEE Student Branch Conference Mikulov 2019

Pages from

6

Pages to

9

Pages count

4

URL

http://www.radio.feec.vutbr.cz/ieee/userfiles/downloads/archive/2019-Mikulov/sbornik.pdf

BibTex

@inproceedings{BUT158994,
  author="Markéta {Jakubíčková} and Helena {Vítková}",
  title="Method for improving the consensus sequence from NGS data based on reads classification",
  booktitle="Proceedings of IEEE Student Branch Conference Mikulov 2019",
  year="2019",
  number="první",
  pages="6--9",
  publisher="Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních technologií",
  address="Brno",
  isbn="978-80-214-5781-2",
  url="http://www.radio.feec.vutbr.cz/ieee/userfiles/downloads/archive/2019-Mikulov/sbornik.pdf"
}