Publication detail

CNproScan: Hybrid CNV detection for bacterial genomes

JUGAS, R. SEDLÁŘ, K. VÍTEK, M. NYKRÝNOVÁ, M. BARTOŇ, V. BEZDÍČEK, M. LENGEROVÁ, M. ŠKUTKOVÁ, H.

Original Title

CNproScan: Hybrid CNV detection for bacterial genomes

Type

journal article in Web of Science

Language

English

Original Abstract

Discovering copy number variation (CNV) in bacteria is not in the spotlight compared to the attention focused on CNV detection in eukaryotes. However, challenges arising from bacterial drug resistance bring further interest to the topic of CNV and its role in drug resistance. General CNV detection methods do not consider bacteria's features and there is space to improve detection accuracy. Here, we present a CNV detection method called CNproScan focused on bacterial genomes. CNproScan implements a hybrid approach and other bacteria-focused features and depends only on NGS data. We benchmarked our method and compared it to the previously published methods and we can resolve to achieve a higher detection rate together with providing other beneficial features, such as CNV classification. Compared with other methods, CNproScan can detect much shorter CNV events.

Keywords

Next-generation sequencing; Copy number variation; Bacteria; Drug resistance

Authors

JUGAS, R.; SEDLÁŘ, K.; VÍTEK, M.; NYKRÝNOVÁ, M.; BARTOŇ, V.; BEZDÍČEK, M.; LENGEROVÁ, M.; ŠKUTKOVÁ, H.

Released

3. 7. 2021

Publisher

Elsevier

ISBN

0888-7543

Periodical

GENOMICS

Year of study

113

Number

5

State

United States of America

Pages from

3103

Pages to

3111

Pages count

9

URL

https://www.sciencedirect.com/science/article/abs/pii/S0888754321002779

BibTex

@article{BUT172131,
  author="Robin {Jugas} and Karel {Sedlář} and Martin {Vítek} and Markéta {Nykrýnová} and Vojtěch {Bartoň} and Matěj {Bezdíček} and Martina {Lengerová} and Helena {Vítková}",
  title="CNproScan: Hybrid CNV detection for bacterial genomes
",
  journal="GENOMICS",
  year="2021",
  volume="113",
  number="5",
  pages="3103--3111",
  doi="10.1016/j.ygeno.2021.06.040",
  issn="0888-7543",
  url="https://www.sciencedirect.com/science/article/abs/pii/S0888754321002779"
}